From 8a11f347f587de42ef1cede1dcccda68ef9c4dde Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 01:58:51 +0000 Subject: [PATCH 01/24] added Makevars for windows --- DESCRIPTION | 3 ++- src/Makevars.win | 3 +++ 2 files changed, 5 insertions(+), 1 deletion(-) create mode 100644 src/Makevars.win diff --git a/DESCRIPTION b/DESCRIPTION index 99b78c9..2b06cd4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -26,7 +26,8 @@ Encoding: UTF-8 RoxygenNote: 7.1.1 LazyData: true Suggests: testthat, - covr + covr, + zlibbioc LinkingTo: Rcpp Collate: allGenerics.R allClasses.R diff --git a/src/Makevars.win b/src/Makevars.win new file mode 100644 index 0000000..8260e47 --- /dev/null +++ b/src/Makevars.win @@ -0,0 +1,3 @@ +PKG_CXXFLAGS += -I${OPEN_BABEL_SRC}${R_ARCH}/include +PKG_LIBS += -L${OPEN_BABEL_BIN}${R_ARCH}/bin -lopenbabel $(shell echo 'zlibbioc::pkgconfig("PKG_LIBS_shared")' |\ +"${R_HOME}/bin/R" --vanilla --slave) From 02a68a186bcc37d553b826b2cfb222b846946685 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 02:07:46 +0000 Subject: [PATCH 02/24] added biocViews to DESCRIPTION --- DESCRIPTION | 1 + 1 file changed, 1 insertion(+) diff --git a/DESCRIPTION b/DESCRIPTION index a6bb16c..594eb7e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,6 +8,7 @@ Authors@R: email = "jsf9@aber.ac.uk") Description: Tools for the putative annotation of high resolution metabolomics m/z. data. +biocViews: MassSpectrometry, Metabolomics URL: https://github.com/jasenfinch/mzAnnotation Depends: R (>= 3.5) Imports: From 070a22c8a37a7f337164311091f3ec55dc46d177 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 02:42:13 +0000 Subject: [PATCH 03/24] added download openbabel binaries in GH actions workflow --- .github/workflows/R-CMD-check.yaml | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 87e1cfb..ee18d9d 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -54,6 +54,13 @@ jobs: key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1-${{ hashFiles('.github/depends.Rds') }} restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-1- + - name: Install Windows system dependencies + if: runner.os == 'Windows' + run: | + curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o openbable-3-build.zip + tar -xf openbabel3-build.zip + echo %cd% + - name: Install Linux system dependencies if: runner.os == 'Linux' run: | From 4f07a10cfa4ad10cb6d9d3231471635d9ce38d80 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 02:48:16 +0000 Subject: [PATCH 04/24] typo fix in GH actions workflow --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index ee18d9d..2883f40 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -57,7 +57,7 @@ jobs: - name: Install Windows system dependencies if: runner.os == 'Windows' run: | - curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o openbable-3-build.zip + curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o openbabel3-build.zip tar -xf openbabel3-build.zip echo %cd% From 28f629dc22a6ae703dcfce217c2eda3b5eb089a3 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 02:54:09 +0000 Subject: [PATCH 05/24] attempt to set openbabel environment bariables for windows build --- .github/workflows/R-CMD-check.yaml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 2883f40..05e79de 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -59,7 +59,8 @@ jobs: run: | curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o openbabel3-build.zip tar -xf openbabel3-build.zip - echo %cd% + setx OPEN_BABEL_SRC ./openbabel3-build/src + setx OPEN_BABEL_BIN ./openbabel3-build/bin - name: Install Linux system dependencies if: runner.os == 'Linux' From 7f0ea2d561f06430be8bbc77627c38a502cea220 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 13:54:10 +0000 Subject: [PATCH 06/24] debugging additions to GH actions workflow for the windows build --- .github/workflows/R-CMD-check.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 05e79de..47d2f2b 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -58,7 +58,10 @@ jobs: if: runner.os == 'Windows' run: | curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o openbabel3-build.zip - tar -xf openbabel3-build.zip + curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip + mkdir openbabel3-build + tar -xf openbabel3-build.zip -C openbabel3-build + Rscript -e "getwd()" setx OPEN_BABEL_SRC ./openbabel3-build/src setx OPEN_BABEL_BIN ./openbabel3-build/bin From 3ac74e11728ef4b37bfbb4d03404430891f99ec1 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 14:09:51 +0000 Subject: [PATCH 07/24] further GH actions workflow debugging additions --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 47d2f2b..feef27a 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -58,7 +58,7 @@ jobs: if: runner.os == 'Windows' run: | curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o openbabel3-build.zip - curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip + dir mkdir openbabel3-build tar -xf openbabel3-build.zip -C openbabel3-build Rscript -e "getwd()" From 4cb724471a81537b6ea828900e93b79d47254125 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 14:19:00 +0000 Subject: [PATCH 08/24] potential fix for GH actions windows build --- .github/workflows/R-CMD-check.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index feef27a..2a50478 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -58,10 +58,8 @@ jobs: if: runner.os == 'Windows' run: | curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o openbabel3-build.zip - dir mkdir openbabel3-build - tar -xf openbabel3-build.zip -C openbabel3-build - Rscript -e "getwd()" + unzip openbabel3-build.zip -d openbabel3-build setx OPEN_BABEL_SRC ./openbabel3-build/src setx OPEN_BABEL_BIN ./openbabel3-build/bin From 95d37431464c46a3c96bb526a81036e1d46348e2 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 14:38:49 +0000 Subject: [PATCH 09/24] file path fixes for GH actions windows build --- .github/workflows/R-CMD-check.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 2a50478..9b766f6 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -57,11 +57,11 @@ jobs: - name: Install Windows system dependencies if: runner.os == 'Windows' run: | - curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o openbabel3-build.zip - mkdir openbabel3-build - unzip openbabel3-build.zip -d openbabel3-build - setx OPEN_BABEL_SRC ./openbabel3-build/src - setx OPEN_BABEL_BIN ./openbabel3-build/bin + curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o D:\a\openbabel3-build.zip + mkdir D:\a\openbabel3-build + unzip D:\a\openbabel3-build.zip -d D:\a\openbabel3-build + setx OPEN_BABEL_SRC D:/a/openbabel3-build/src + setx OPEN_BABEL_BIN D:/a/openbabel3-build/bin - name: Install Linux system dependencies if: runner.os == 'Linux' From 8c9d97c88bb04890bcf013251b1881d101cb8b02 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 14:56:18 +0000 Subject: [PATCH 10/24] debugging additions for GH actions Windows build --- .github/workflows/R-CMD-check.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 9b766f6..0c20e47 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -62,6 +62,7 @@ jobs: unzip D:\a\openbabel3-build.zip -d D:\a\openbabel3-build setx OPEN_BABEL_SRC D:/a/openbabel3-build/src setx OPEN_BABEL_BIN D:/a/openbabel3-build/bin + set - name: Install Linux system dependencies if: runner.os == 'Linux' From ed637e1e3cf5b0b7c48d572e5c17dfd975be39e1 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 15:04:51 +0000 Subject: [PATCH 11/24] debug GH actions workflow fix --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 0c20e47..6a867e4 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -62,7 +62,7 @@ jobs: unzip D:\a\openbabel3-build.zip -d D:\a\openbabel3-build setx OPEN_BABEL_SRC D:/a/openbabel3-build/src setx OPEN_BABEL_BIN D:/a/openbabel3-build/bin - set + SET - name: Install Linux system dependencies if: runner.os == 'Linux' From 5f19fdd858e89916cffd2b3719b55a2081037cd5 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 15:18:46 +0000 Subject: [PATCH 12/24] Windows GH actions build environment debug fix --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 6a867e4..052786c 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -62,7 +62,7 @@ jobs: unzip D:\a\openbabel3-build.zip -d D:\a\openbabel3-build setx OPEN_BABEL_SRC D:/a/openbabel3-build/src setx OPEN_BABEL_BIN D:/a/openbabel3-build/bin - SET + env - name: Install Linux system dependencies if: runner.os == 'Linux' From 299a80b306950ac9e2dbdd0b78343adf2f933bd2 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 15:32:58 +0000 Subject: [PATCH 13/24] attempt to set correctly set Openbabel system environment variables for Windows GH actions build --- .github/workflows/R-CMD-check.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 052786c..9b9ef6e 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -60,8 +60,8 @@ jobs: curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o D:\a\openbabel3-build.zip mkdir D:\a\openbabel3-build unzip D:\a\openbabel3-build.zip -d D:\a\openbabel3-build - setx OPEN_BABEL_SRC D:/a/openbabel3-build/src - setx OPEN_BABEL_BIN D:/a/openbabel3-build/bin + setx OPEN_BABEL_SRC D:/a/openbabel3-build/src /m + setx OPEN_BABEL_BIN D:/a/openbabel3-build/bin /m env - name: Install Linux system dependencies From 59b32fa760e3ab6e3781d9a7b88beaa4991c0116 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Sun, 24 Jan 2021 15:51:25 +0000 Subject: [PATCH 14/24] Potential fix for Openbabel environment variables in Windows GH actions build --- .github/workflows/R-CMD-check.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 9b9ef6e..1493b0b 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -60,9 +60,6 @@ jobs: curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o D:\a\openbabel3-build.zip mkdir D:\a\openbabel3-build unzip D:\a\openbabel3-build.zip -d D:\a\openbabel3-build - setx OPEN_BABEL_SRC D:/a/openbabel3-build/src /m - setx OPEN_BABEL_BIN D:/a/openbabel3-build/bin /m - env - name: Install Linux system dependencies if: runner.os == 'Linux' @@ -87,6 +84,8 @@ jobs: - name: Check env: _R_CHECK_CRAN_INCOMING_REMOTE_: false + OPEN_BABEL_SRC: D:/a/openbabel3-build/src + OPEN_BABEL_BIN: D:/a/openbabel3-build/bin run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check") shell: Rscript {0} From e1daf2a68b89e967679512f85acd8c4e918bc758 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Mon, 25 Jan 2021 11:31:13 +0000 Subject: [PATCH 15/24] random fix for Windows GH action build --- .github/workflows/R-CMD-check.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 1493b0b..c86cceb 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -60,6 +60,7 @@ jobs: curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o D:\a\openbabel3-build.zip mkdir D:\a\openbabel3-build unzip D:\a\openbabel3-build.zip -d D:\a\openbabel3-build + dir - name: Install Linux system dependencies if: runner.os == 'Linux' From 490e47f7c5aa473c43808fe4ca9d85b305a8011c Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Mon, 25 Jan 2021 11:42:41 +0000 Subject: [PATCH 16/24] Switch to using R to prepare Openbabel binaries for Wondows GH build --- .github/workflows/R-CMD-check.yaml | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index c86cceb..426f062 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -57,10 +57,9 @@ jobs: - name: Install Windows system dependencies if: runner.os == 'Windows' run: | - curl.exe -L https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip -o D:\a\openbabel3-build.zip - mkdir D:\a\openbabel3-build - unzip D:\a\openbabel3-build.zip -d D:\a\openbabel3-build - dir + download.file('https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip','D:\a\openbabel3-build.zip') + unzip('D:\a\openbabel3-build.zip',exdir = ''D:\a\openbabel3-build') + shell: Rscript {0} - name: Install Linux system dependencies if: runner.os == 'Linux' From abb4c28e6f2e9b93dd90ffb7fba4186ad2c6c14c Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Mon, 25 Jan 2021 11:43:25 +0000 Subject: [PATCH 17/24] fix typo --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 426f062..7e7e357 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -58,7 +58,7 @@ jobs: if: runner.os == 'Windows' run: | download.file('https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip','D:\a\openbabel3-build.zip') - unzip('D:\a\openbabel3-build.zip',exdir = ''D:\a\openbabel3-build') + unzip('D:\a\openbabel3-build.zip',exdir = 'D:\a\openbabel3-build') shell: Rscript {0} - name: Install Linux system dependencies From 61933608bb88ee223b7b05cda138575e442b4948 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Mon, 25 Jan 2021 11:51:57 +0000 Subject: [PATCH 18/24] fixed backslashes in file paths for Windows GH actions build --- .github/workflows/R-CMD-check.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 7e7e357..0586597 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -57,8 +57,8 @@ jobs: - name: Install Windows system dependencies if: runner.os == 'Windows' run: | - download.file('https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip','D:\a\openbabel3-build.zip') - unzip('D:\a\openbabel3-build.zip',exdir = 'D:\a\openbabel3-build') + download.file('https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip','D:/a/openbabel3-build.zip') + unzip('D:/a/openbabel3-build.zip',exdir = 'D:/a/openbabel3-build') shell: Rscript {0} - name: Install Linux system dependencies From fda9a0cad9311c835b4351dba4273e67cf52ebd8 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Mon, 25 Jan 2021 12:43:21 +0000 Subject: [PATCH 19/24] openbabel binary decompression fix for Windows GH actions workflow --- .github/workflows/R-CMD-check.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index 0586597..195eccd 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -58,7 +58,7 @@ jobs: if: runner.os == 'Windows' run: | download.file('https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip','D:/a/openbabel3-build.zip') - unzip('D:/a/openbabel3-build.zip',exdir = 'D:/a/openbabel3-build') + untar('D:/a/openbabel3-build.zip',exdir = 'D:/a/openbabel3-build') shell: Rscript {0} - name: Install Linux system dependencies From 1a2fb32d8a623efe65019b83929cf0b86c519d07 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Wed, 17 Feb 2021 22:52:54 +0000 Subject: [PATCH 20/24] update README --- README.Rmd | 1 + README.md | 16 ++++------------ 2 files changed, 5 insertions(+), 12 deletions(-) diff --git a/README.Rmd b/README.Rmd index e366060..0ff3701 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,6 +16,7 @@ An R package containing tools for putative annotation of accurate m/z from elect ### Installation To install run: + ```R devtools::install_github('jasenfinch/mzAnnotation') ``` diff --git a/README.md b/README.md index 4d7bed2..71729f8 100644 --- a/README.md +++ b/README.md @@ -21,9 +21,7 @@ devtools::install_github('jasenfinch/mzAnnotation') Available tools include: - - Adduct, isotope and biotransfromation relationship prediction - - +- Adduct, isotope and biotransfromation relationship prediction ``` r res <- relationshipCalculator(c(132.03023,168.00691)) @@ -36,9 +34,7 @@ res #> # … with 2 more variables: Transformation2 , Error ``` - - Molecular formula generation - - +- Molecular formula generation ``` r res <- generateMF(342.11621, @@ -51,9 +47,7 @@ res #> 1 C12H22O11 342. 0 ``` - - Isotope distribution calculation - - +- Isotope distribution calculation ``` r res <- isotopeDistribution(MF = 'C4H5O5',charge = -1) @@ -71,9 +65,7 @@ res #> 8 13C 1; 17O 1 135. 0.0000900 0.0000850 ``` - - Putative ionisation product searches - - +- Putative ionisation product searches ``` r db <- metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES)) From 97aa68649c9f1c67472e5607b0ab4cb26232a1f1 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Wed, 17 Feb 2021 22:54:53 +0000 Subject: [PATCH 21/24] bumped version to 1.7.3 --- DESCRIPTION | 2 +- README.Rmd | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d944b43..a991e21 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: mzAnnotation Title: Signal Annotation Tools for High Resolution Metabolomics -Version: 1.7.2 +Version: 1.7.3 Authors@R: person(given = "Jasen", family = "Finch", diff --git a/README.Rmd b/README.Rmd index 0ff3701..d9fc597 100644 --- a/README.Rmd +++ b/README.Rmd @@ -30,6 +30,7 @@ library(mzAnnotation) ``` * Adduct, isotope and biotransfromation relationship prediction + ```{r} res <- relationshipCalculator(c(132.03023,168.00691)) @@ -37,6 +38,7 @@ res ``` * Molecular formula generation + ```{r} res <- generateMF(342.11621, element_max = c(C = 12,H = 22,N = 0, @@ -45,12 +47,14 @@ res ``` * Isotope distribution calculation + ```{r} res <- isotopeDistribution(MF = 'C4H5O5',charge = -1) res ``` * Putative ionisation product searches + ```{r} db <- metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES)) res <- PIPsearch(db = db, From 4951358f6efb180ed8b42c96b0f1a0141d43f4ca Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Wed, 17 Feb 2021 22:58:07 +0000 Subject: [PATCH 22/24] added package news --- NEWS.md | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 NEWS.md diff --git a/NEWS.md b/NEWS.md new file mode 100644 index 0000000..61b73cb --- /dev/null +++ b/NEWS.md @@ -0,0 +1,5 @@ +# mzAnnotation 1.7.3 + +* Added a `NEWS.md` file to track changes to the package. + +* Added a `pkgdown` site available at https://jasenfinch.github.io/mzAnnotation/. From 941626bb74eaf374f42cb4e7028c16605247c8c7 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Wed, 17 Feb 2021 23:31:14 +0000 Subject: [PATCH 23/24] added pkgdown site --- R/PIPsearch.R | 2 +- R/RcppExports.R | 8 +- R/adductTransfromMF.R | 2 +- R/allClasses.R | 2 +- R/aminoAcids.R | 2 +- R/calcAccurateMass.R | 2 +- R/calcAdducts.R | 2 +- R/calcM.R | 2 +- R/calcMZ.R | 2 +- R/convert.R | 2 +- R/data.R | 8 +- R/descriptors.R | 3 +- R/filter-methods.R | 10 +- R/generateMF.R | 2 +- R/get-methods.R | 4 +- R/ionisationProducts.R | 2 +- R/isotopeDistribution.R | 2 +- R/metaboliteDB.R | 2 +- R/mzAnnotation.R | 2 - R/ppmError.R | 2 +- R/transformMF.R | 2 +- docs/404.html | 148 ++++ docs/LICENSE-text.html | 822 ++++++++++++++++++ docs/authors.html | 147 ++++ docs/bootstrap-toc.css | 60 ++ docs/bootstrap-toc.js | 159 ++++ docs/docsearch.css | 148 ++++ docs/docsearch.js | 85 ++ docs/index.html | 198 +++++ docs/link.svg | 12 + docs/news/index.html | 154 ++++ docs/pkgdown.css | 367 ++++++++ docs/pkgdown.js | 108 +++ docs/pkgdown.yml | 6 + docs/reference/MetaboliteDatabase-class.html | 153 ++++ docs/reference/PIPsearch.html | 211 +++++ docs/reference/Rplot001.png | Bin 0 -> 1011 bytes docs/reference/adductTransformMF.html | 173 ++++ docs/reference/adducts.html | 170 ++++ docs/reference/aminoAcids.html | 165 ++++ docs/reference/calcAccurateMass.html | 173 ++++ docs/reference/calcAdducts.html | 177 ++++ docs/reference/calcM.html | 197 +++++ docs/reference/calcMZ.html | 197 +++++ docs/reference/convert.html | 173 ++++ docs/reference/descriptors.html | 190 ++++ docs/reference/elements.html | 157 ++++ docs/reference/filterACCESSIONS.html | 173 ++++ docs/reference/filterER.html | 173 ++++ docs/reference/filterIP.html | 174 ++++ docs/reference/filterMF.html | 173 ++++ docs/reference/filterMR.html | 177 ++++ docs/reference/generateMF.html | 203 +++++ docs/reference/getAccessions.html | 165 ++++ docs/reference/getDescriptors.html | 165 ++++ docs/reference/index.html | 365 ++++++++ docs/reference/ionisationProducts.html | 182 ++++ docs/reference/isotopeDistribution.html | 180 ++++ docs/reference/isotopes.html | 163 ++++ docs/reference/metaboliteDB.html | 177 ++++ docs/reference/mzAnnotation.html | 153 ++++ docs/reference/ppmError.html | 169 ++++ docs/reference/ppmRange.html | 174 ++++ docs/reference/relationshipCalculator.html | 224 +++++ .../show-MetaboliteDatabase-method.html | 163 ++++ docs/reference/smartsSearch.html | 169 ++++ docs/reference/smileToAccurateMass.html | 165 ++++ docs/reference/smileToMF.html | 165 ++++ docs/reference/transformMF.html | 181 ++++ docs/reference/transformations.html | 169 ++++ man/MetaboliteDatabase-class.Rd | 4 +- man/PIPsearch.Rd | 4 +- man/adductTransformMF.Rd | 2 +- man/adducts.Rd | 2 +- man/aminoAcids.Rd | 2 +- man/calcAccurateMass.Rd | 2 +- man/calcAdducts.Rd | 2 +- man/calcM.Rd | 2 +- man/calcMZ.Rd | 2 +- man/convert.Rd | 2 +- man/descriptors.Rd | 4 +- man/elements.Rd | 2 +- man/filterACCESSIONS.Rd | 2 +- man/filterER.Rd | 2 +- man/filterIP.Rd | 2 +- man/filterMF.Rd | 2 +- man/filterMR.Rd | 2 +- man/generateMF.Rd | 2 +- man/getAccessions.Rd | 2 +- man/getDescriptors.Rd | 2 +- man/ionisationProducts.Rd | 2 +- man/isotopeDistribution.Rd | 4 +- man/isotopes.Rd | 2 +- man/metaboliteDB.Rd | 2 +- man/mzAnnotation.Rd | 8 - man/ppmError.Rd | 2 +- man/ppmRange.Rd | 2 +- man/smartsSearch.Rd | 2 +- man/smileToAccurateMass.Rd | 2 +- man/smileToMF.Rd | 2 +- man/transformMF.Rd | 2 +- man/transformations.Rd | 2 +- src/conversion.cpp | 4 +- src/descriptors.cpp | 2 +- src/ppmRange.cpp | 2 +- 105 files changed, 8822 insertions(+), 81 deletions(-) create mode 100644 docs/404.html create mode 100644 docs/LICENSE-text.html create mode 100644 docs/authors.html create mode 100644 docs/bootstrap-toc.css create mode 100644 docs/bootstrap-toc.js create mode 100644 docs/docsearch.css create mode 100644 docs/docsearch.js create mode 100644 docs/index.html create mode 100644 docs/link.svg create mode 100644 docs/news/index.html create mode 100644 docs/pkgdown.css create mode 100644 docs/pkgdown.js create mode 100644 docs/pkgdown.yml create mode 100644 docs/reference/MetaboliteDatabase-class.html create mode 100644 docs/reference/PIPsearch.html create mode 100644 docs/reference/Rplot001.png create mode 100644 docs/reference/adductTransformMF.html create mode 100644 docs/reference/adducts.html create mode 100644 docs/reference/aminoAcids.html create mode 100644 docs/reference/calcAccurateMass.html create mode 100644 docs/reference/calcAdducts.html create mode 100644 docs/reference/calcM.html create mode 100644 docs/reference/calcMZ.html create mode 100644 docs/reference/convert.html create mode 100644 docs/reference/descriptors.html create mode 100644 docs/reference/elements.html create mode 100644 docs/reference/filterACCESSIONS.html create mode 100644 docs/reference/filterER.html create mode 100644 docs/reference/filterIP.html create mode 100644 docs/reference/filterMF.html create mode 100644 docs/reference/filterMR.html create mode 100644 docs/reference/generateMF.html create mode 100644 docs/reference/getAccessions.html create mode 100644 docs/reference/getDescriptors.html create mode 100644 docs/reference/index.html create mode 100644 docs/reference/ionisationProducts.html create mode 100644 docs/reference/isotopeDistribution.html create mode 100644 docs/reference/isotopes.html create mode 100644 docs/reference/metaboliteDB.html create mode 100644 docs/reference/mzAnnotation.html create mode 100644 docs/reference/ppmError.html create mode 100644 docs/reference/ppmRange.html create mode 100644 docs/reference/relationshipCalculator.html create mode 100644 docs/reference/show-MetaboliteDatabase-method.html create mode 100644 docs/reference/smartsSearch.html create mode 100644 docs/reference/smileToAccurateMass.html create mode 100644 docs/reference/smileToMF.html create mode 100644 docs/reference/transformMF.html create mode 100644 docs/reference/transformations.html delete mode 100644 man/mzAnnotation.Rd diff --git a/R/PIPsearch.R b/R/PIPsearch.R index e2372ba..99f8a12 100644 --- a/R/PIPsearch.R +++ b/R/PIPsearch.R @@ -1,4 +1,4 @@ -#' Putative Ionisation Product searching +#' Putative ionisation product search #' @rdname PIPsearch #' @param db object of class \code{MetaboliteDatabase}. #' @param mz the accurate m/z to search. diff --git a/R/RcppExports.R b/R/RcppExports.R index e3e8e9d..ae6cde4 100644 --- a/R/RcppExports.R +++ b/R/RcppExports.R @@ -9,7 +9,7 @@ cnvrt <- function(input, inputType, outputType) { .Call('_mzAnnotation_cnvrt', PACKAGE = 'mzAnnotation', input, inputType, outputType) } -#' smileToMF +#' Convert SMILES to molecular formula #' @description convert a smile to a molecular formula #' @param smile a valid SMILE #' @examples @@ -19,7 +19,7 @@ smileToMF <- function(smile) { .Call('_mzAnnotation_smileToMF', PACKAGE = 'mzAnnotation', smile) } -#' smileToAccurateMass +#' Convert SMILES to accurate mass #' @description convert a smile to an accurate mass #' @param smile a valid SMILE #' @examples @@ -29,7 +29,7 @@ smileToAccurateMass <- function(smile) { .Call('_mzAnnotation_smileToAccurateMass', PACKAGE = 'mzAnnotation', smile) } -#' smartsSearch +#' SMARTS substructure search #' @description SMARTS substructure searching for SMILES. #' @param smile a valid SMILE #' @param smart a valid SMARTS symbol @@ -44,7 +44,7 @@ descriptor <- function(smile, desc) { .Call('_mzAnnotation_descriptor', PACKAGE = 'mzAnnotation', smile, desc) } -#' ppmRange +#' Calculate a PPM error range #' @description Calculate the upper and lower ppm boundaries for a given m/z #' @param mz the m/z for which to calculate the range #' @param ppm the ppm diff --git a/R/adductTransfromMF.R b/R/adductTransfromMF.R index 028c9be..df8cc43 100644 --- a/R/adductTransfromMF.R +++ b/R/adductTransfromMF.R @@ -1,4 +1,4 @@ -#' adductTransformMF +#' Molecular formula adduct transformation #' @description adduct transform a molecular formula. #' @param MF molecular formula to transform. #' @param adduct adduct to use for transformation. diff --git a/R/allClasses.R b/R/allClasses.R index 9bc66ee..b3c464f 100644 --- a/R/allClasses.R +++ b/R/allClasses.R @@ -1,7 +1,7 @@ # setOldClass('tbl_dbi') # setClassUnion('metabolite_table',c('tbl_df','tbl_dbi')) -#' MetaboliteDatabase +#' Metabolite database class #' @export setClass('MetaboliteDatabase', diff --git a/R/aminoAcids.R b/R/aminoAcids.R index 56307b7..7d2bf3c 100644 --- a/R/aminoAcids.R +++ b/R/aminoAcids.R @@ -1,4 +1,4 @@ -#' aminoAcids +#' Example amino acids #' @description Chemical structures of the essential amino acids #' @format a tibble containing 20 rows and 6 columns #' \describe{ diff --git a/R/calcAccurateMass.R b/R/calcAccurateMass.R index 46f59ee..19c3109 100644 --- a/R/calcAccurateMass.R +++ b/R/calcAccurateMass.R @@ -1,4 +1,4 @@ -#' calcAccurateMass +#' Calculate molecular formula accurate mass #' @description calculate the accurate mass of a given molecular formula #' @param MF molecular formula for which to calculate the accrate mass #' @param charge charge of the given molecular formula diff --git a/R/calcAdducts.R b/R/calcAdducts.R index 690f75f..b8ef6cc 100644 --- a/R/calcAdducts.R +++ b/R/calcAdducts.R @@ -1,4 +1,4 @@ -#' calcAdducts +#' Calculate adducts #' @rdname calcAdducts #' @description Calculate ionisation products for given database accession. #' @param db object of class \code{MetaboliteDatabase} diff --git a/R/calcM.R b/R/calcM.R index 38af7dc..bca8db2 100644 --- a/R/calcM.R +++ b/R/calcM.R @@ -1,4 +1,4 @@ -#' calcM +#' Calculate the mass of an m/z #' @description calculate M for a given m/z, adduct, isotope and transformation #' @param mz m/z for which to calculate M #' @param adduct adduct to apply diff --git a/R/calcMZ.R b/R/calcMZ.R index eeea1cb..17fed1c 100644 --- a/R/calcMZ.R +++ b/R/calcMZ.R @@ -1,4 +1,4 @@ -#' calcM +#' Calculate the m/z of a mass #' @description calculate an m/z for a given M, adduct, isotope and transformation #' @param M M for which to calculate an m/z #' @param adduct adduct to apply diff --git a/R/convert.R b/R/convert.R index 5bc5144..df3b527 100644 --- a/R/convert.R +++ b/R/convert.R @@ -1,4 +1,4 @@ -#' convert +#' Convert chemical notation #' @description convert between SMILES and Inchi and to InchiKey #' @param input a valid SMILE or Inchi #' @param inputType either "smiles" or "inchi", denoting the input type diff --git a/R/data.R b/R/data.R index 98c38ed..3f6e8e0 100644 --- a/R/data.R +++ b/R/data.R @@ -1,4 +1,4 @@ -#' adducts +#' Adduct formation rules #' @description Formation rules for electrospray ionisation adducts #' @format A tibble containing 58 rows and 6 columns #' \describe{ @@ -19,7 +19,7 @@ adducts <- function(){ return(Adducts) } -#' elements +#' Elemental information #' @description Elemental information #' @format A tibble containing 31 rows and 5 columns. #' @export @@ -28,7 +28,7 @@ elements <- function(){ return(Elements) } -#' isotopes +#' Isotopic rules #' @description Isotope rules #' @format A tibble containing 8 rows and 3 columns. #' \describe{ @@ -42,7 +42,7 @@ isotopes <- function(){ return(Isotopes) } -#' transformations +#' Transformation rules #' @description Transformation rules #' @format A tibble containing 12 rows and 9 columns. #' \describe{ diff --git a/R/descriptors.R b/R/descriptors.R index 76639cc..474a39a 100644 --- a/R/descriptors.R +++ b/R/descriptors.R @@ -1,5 +1,4 @@ -#' convert SMILES to a series of molecular descriptors -#' +#' Molecular descriptors #' @param SMILES a character vector of valid SMILES #' @importFrom dplyr mutate #' @importFrom parallel makeCluster parLapply stopCluster diff --git a/R/filter-methods.R b/R/filter-methods.R index 1834c82..510949e 100644 --- a/R/filter-methods.R +++ b/R/filter-methods.R @@ -1,4 +1,4 @@ -#' filterMR +#' Filter a mass range #' @rdname filterMR #' @description Filter a MetaboliteDatabase for a given mass range. #' @param db S4 object of class MetaboliteDatabase @@ -23,7 +23,7 @@ setMethod('filterMR',signature = 'MetaboliteDatabase', } ) -#' filterER +#' Filter using an elemental rule #' @rdname filterER #' @description Filter a MetaboliteDatabase based on an elemental rule. #' @param db S4 object of class MetaboliteDatabase @@ -50,7 +50,7 @@ setMethod('filterER',signature = 'MetaboliteDatabase', } ) -#' filterIP +#' Filter using an ionisation rule #' @rdname filterIP #' @description Filter MetaboliteDatabase based on an ionisation rule #' @param db S4 object of class MetaboliteDatabase @@ -75,7 +75,7 @@ setMethod('filterIP',signature = 'MetaboliteDatabase', } ) -#' filterACCESSIONS +#' Filter accessions #' @rdname filterACCESSIONS #' @description Filter a MetaboliteDatabase based on given accession IDs. #' @param db S4 object of class MetaboliteDatabase @@ -97,7 +97,7 @@ setMethod('filterACCESSIONS',signature = 'MetaboliteDatabase', } ) -#' filterMF +#' Filter a molecular formula #' @rdname filterMF #' @description Filter a MetaboliteDatabase based on given molecular formulas #' @param db S4 object of class MetaboliteDatabase diff --git a/R/generateMF.R b/R/generateMF.R index f209477..023c633 100644 --- a/R/generateMF.R +++ b/R/generateMF.R @@ -1,4 +1,4 @@ -#' generateMF +#' Molecular formula generation #' @description Molecular formula generation #' @param mass accurate mass #' @param ppm ppm tolerance diff --git a/R/get-methods.R b/R/get-methods.R index 255ad08..09f2dd6 100644 --- a/R/get-methods.R +++ b/R/get-methods.R @@ -1,4 +1,4 @@ -#' getAccessions-MetaboliteDatabase +#' Retrieve accessions #' @rdname getAccessions #' @description return accession data table from MetaboliteDatabase object #' @param db MetaboliteDatabase @@ -10,7 +10,7 @@ setMethod('getAccessions',signature = 'MetaboliteDatabase', } ) -#' getDescriptors-MetaboliteDatabase +#' Retrieve descriptors #' @rdname getDescriptors #' @description return descriptor data table from MetaboliteDatabase object #' @param db MetaboliteDatabase diff --git a/R/ionisationProducts.R b/R/ionisationProducts.R index 9ab2a39..75c6eb8 100644 --- a/R/ionisationProducts.R +++ b/R/ionisationProducts.R @@ -1,4 +1,4 @@ -#' Ionisation Products +#' Ionisation products #' @description Calculate ionisation products for a given SMILES. #' @param SMILES a valid SMILES string #' @param adductTable table of adduct rules. Defaults to adducts() diff --git a/R/isotopeDistribution.R b/R/isotopeDistribution.R index 0c48ec9..063a449 100644 --- a/R/isotopeDistribution.R +++ b/R/isotopeDistribution.R @@ -1,4 +1,4 @@ -#' Isotopic Distribution Calculator +#' Isotopic distribution calculator #' @param MF the molecular formular to generate the isotope distribution #' @param charge the charge of the molecular formula #' @param limit the relative abundance threshold diff --git a/R/metaboliteDB.R b/R/metaboliteDB.R index acfa1ba..bf88279 100644 --- a/R/metaboliteDB.R +++ b/R/metaboliteDB.R @@ -1,4 +1,4 @@ -#' metaboliteDB +#' Create a metabolite database #' @description Build a metabolite database ready for use. #' @param accessions tibble containing accession information. If \code{type = 'remote'} this should be the name of the table containing the accession information within the SQL database. #' @param descriptors tibble containing descriptor information as returned by \code{descriptors()}. If \code{type = 'remote'} this should be the name of the table containing the descriptor information within the SQL database. diff --git a/R/mzAnnotation.R b/R/mzAnnotation.R index f996c29..d0142e5 100644 --- a/R/mzAnnotation.R +++ b/R/mzAnnotation.R @@ -1,5 +1,3 @@ -#' mzAnnotation -#' @name mzAnnotation #' @useDynLib mzAnnotation #' @importFrom Rcpp evalCpp diff --git a/R/ppmError.R b/R/ppmError.R index 63e6530..f47cf41 100644 --- a/R/ppmError.R +++ b/R/ppmError.R @@ -1,4 +1,4 @@ -#' ppmError +#' Calculate PPM error #' @description Calculate ppmError between a measured and theoretical m/z #' @param measured measured m/z #' @param theoretical theoretical m/z diff --git a/R/transformMF.R b/R/transformMF.R index 946e56d..4c1a947 100644 --- a/R/transformMF.R +++ b/R/transformMF.R @@ -1,4 +1,4 @@ -#' transformMF +#' Transform a molecular formula #' @description transform a molecular formula #' @param MF molecular formula to transform #' @param transformation transformation to apply diff --git a/docs/404.html b/docs/404.html new file mode 100644 index 0000000..35c17eb --- /dev/null +++ b/docs/404.html @@ -0,0 +1,148 @@ + + + + + + + + +Page not found (404) • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
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+  If you develop a new program, and you want it to be of the greatest
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+
+Also add information on how to contact you by electronic and paper mail.
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+  If the program does terminal interaction, make it output a short
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+    <program>  Copyright (C) <year>  <name of author>
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+The hypothetical commands `show w' and `show c' should show the appropriate
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+
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+For more information on this, and how to apply and follow the GNU GPL, see
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+
+  The GNU General Public License does not permit incorporating your program
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+<http://www.gnu.org/philosophy/why-not-lgpl.html>.
+
+ +
+ + + +
+ + + +
+
+

Developed by Jasen Finch.

+
+ +
+

Site built with pkgdown 1.6.1.

+
+ +
+
+ + + + + + + + diff --git a/docs/authors.html b/docs/authors.html new file mode 100644 index 0000000..a7cfab4 --- /dev/null +++ b/docs/authors.html @@ -0,0 +1,147 @@ + + + + + + + + +Authors • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Authors

+
+ +
    +
  • +

    Jasen Finch. Author, maintainer. +

    +
    • +
+ +
+ +
+ + + +
+
+

Developed by Jasen Finch.

+
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+

Site built with pkgdown 1.6.1.

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+ +
+
+ + + + + + + + diff --git a/docs/bootstrap-toc.css b/docs/bootstrap-toc.css new file mode 100644 index 0000000..5a85941 --- /dev/null +++ b/docs/bootstrap-toc.css @@ -0,0 +1,60 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ + +/* modified from https://github.com/twbs/bootstrap/blob/94b4076dd2efba9af71f0b18d4ee4b163aa9e0dd/docs/assets/css/src/docs.css#L548-L601 */ + +/* All levels of nav */ +nav[data-toggle='toc'] .nav > li > a { + display: block; + padding: 4px 20px; + font-size: 13px; + font-weight: 500; + color: #767676; +} +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 19px; + color: #563d7c; + text-decoration: none; + background-color: transparent; + border-left: 1px solid #563d7c; +} +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 18px; + font-weight: bold; + color: #563d7c; + background-color: transparent; + border-left: 2px solid #563d7c; +} + +/* Nav: second level (shown on .active) */ +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} +nav[data-toggle='toc'] .nav .nav > li > a { + padding-top: 1px; + padding-bottom: 1px; + padding-left: 30px; + font-size: 12px; + font-weight: normal; +} +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 29px; +} +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 28px; + font-weight: 500; +} + +/* from https://github.com/twbs/bootstrap/blob/e38f066d8c203c3e032da0ff23cd2d6098ee2dd6/docs/assets/css/src/docs.css#L631-L634 */ +nav[data-toggle='toc'] .nav > .active > ul { + display: block; +} diff --git a/docs/bootstrap-toc.js b/docs/bootstrap-toc.js new file mode 100644 index 0000000..1cdd573 --- /dev/null +++ b/docs/bootstrap-toc.js @@ -0,0 +1,159 @@ +/*! + * Bootstrap Table of Contents v0.4.1 (http://afeld.github.io/bootstrap-toc/) + * Copyright 2015 Aidan Feldman + * Licensed under MIT (https://github.com/afeld/bootstrap-toc/blob/gh-pages/LICENSE.md) */ +(function() { + 'use strict'; + + window.Toc = { + helpers: { + // return all matching elements in the set, or their descendants + findOrFilter: function($el, selector) { + // http://danielnouri.org/notes/2011/03/14/a-jquery-find-that-also-finds-the-root-element/ + // http://stackoverflow.com/a/12731439/358804 + var $descendants = $el.find(selector); + return $el.filter(selector).add($descendants).filter(':not([data-toc-skip])'); + }, + + generateUniqueIdBase: function(el) { + var text = $(el).text(); + var anchor = text.trim().toLowerCase().replace(/[^A-Za-z0-9]+/g, '-'); + return anchor || el.tagName.toLowerCase(); + }, + + generateUniqueId: function(el) { + var anchorBase = this.generateUniqueIdBase(el); + for (var i = 0; ; i++) { + var anchor = anchorBase; + if (i > 0) { + // add suffix + anchor += '-' + i; + } + // check if ID already exists + if (!document.getElementById(anchor)) { + return anchor; + } + } + }, + + generateAnchor: function(el) { + if (el.id) { + return el.id; + } else { + var anchor = this.generateUniqueId(el); + el.id = anchor; + return anchor; + } + }, + + createNavList: function() { + return $('
    '); + }, + + createChildNavList: function($parent) { + var $childList = this.createNavList(); + $parent.append($childList); + return $childList; + }, + + generateNavEl: function(anchor, text) { + var $a = $(''); + $a.attr('href', '#' + anchor); + $a.text(text); + var $li = $('
  • '); + $li.append($a); + return $li; + }, + + generateNavItem: function(headingEl) { + var anchor = this.generateAnchor(headingEl); + var $heading = $(headingEl); + var text = $heading.data('toc-text') || $heading.text(); + return this.generateNavEl(anchor, text); + }, + + // Find the first heading level (`

    `, then `

    `, etc.) that has more than one element. Defaults to 1 (for `

    `). + getTopLevel: function($scope) { + for (var i = 1; i <= 6; i++) { + var $headings = this.findOrFilter($scope, 'h' + i); + if ($headings.length > 1) { + return i; + } + } + + return 1; + }, + + // returns the elements for the top level, and the next below it + getHeadings: function($scope, topLevel) { + var topSelector = 'h' + topLevel; + + var secondaryLevel = topLevel + 1; + var secondarySelector = 'h' + secondaryLevel; + + return this.findOrFilter($scope, topSelector + ',' + secondarySelector); + }, + + getNavLevel: function(el) { + return parseInt(el.tagName.charAt(1), 10); + }, + + populateNav: function($topContext, topLevel, $headings) { + var $context = $topContext; + var $prevNav; + + var helpers = this; + $headings.each(function(i, el) { + var $newNav = helpers.generateNavItem(el); + var navLevel = helpers.getNavLevel(el); + + // determine the proper $context + if (navLevel === topLevel) { + // use top level + $context = $topContext; + } else if ($prevNav && $context === $topContext) { + // create a new level of the tree and switch to it + $context = helpers.createChildNavList($prevNav); + } // else use the current $context + + $context.append($newNav); + + $prevNav = $newNav; + }); + }, + + parseOps: function(arg) { + var opts; + if (arg.jquery) { + opts = { + $nav: arg + }; + } else { + opts = arg; + } + opts.$scope = opts.$scope || $(document.body); + return opts; + } + }, + + // accepts a jQuery object, or an options object + init: function(opts) { + opts = this.helpers.parseOps(opts); + + // ensure that the data attribute is in place for styling + opts.$nav.attr('data-toggle', 'toc'); + + var $topContext = this.helpers.createChildNavList(opts.$nav); + var topLevel = this.helpers.getTopLevel(opts.$scope); + var $headings = this.helpers.getHeadings(opts.$scope, topLevel); + this.helpers.populateNav($topContext, topLevel, $headings); + } + }; + + $(function() { + $('nav[data-toggle="toc"]').each(function(i, el) { + var $nav = $(el); + Toc.init($nav); + }); + }); +})(); diff --git a/docs/docsearch.css b/docs/docsearch.css new file mode 100644 index 0000000..e5f1fe1 --- /dev/null +++ b/docs/docsearch.css @@ -0,0 +1,148 @@ +/* Docsearch -------------------------------------------------------------- */ +/* + Source: https://github.com/algolia/docsearch/ + License: MIT +*/ + +.algolia-autocomplete { + display: block; + -webkit-box-flex: 1; + -ms-flex: 1; + flex: 1 +} + +.algolia-autocomplete .ds-dropdown-menu { + width: 100%; + min-width: none; + max-width: none; + padding: .75rem 0; + background-color: #fff; + background-clip: padding-box; + border: 1px solid rgba(0, 0, 0, .1); + box-shadow: 0 .5rem 1rem rgba(0, 0, 0, .175); +} + +@media (min-width:768px) { + .algolia-autocomplete .ds-dropdown-menu { + width: 175% + } +} + +.algolia-autocomplete .ds-dropdown-menu::before { + display: none +} + +.algolia-autocomplete .ds-dropdown-menu [class^=ds-dataset-] { + padding: 0; + background-color: rgb(255,255,255); + border: 0; + max-height: 80vh; +} + +.algolia-autocomplete .ds-dropdown-menu .ds-suggestions { + margin-top: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion { + padding: 0; + overflow: visible +} + +.algolia-autocomplete .algolia-docsearch-suggestion--category-header { + padding: .125rem 1rem; + margin-top: 0; + font-size: 1.3em; + font-weight: 500; + color: #00008B; + border-bottom: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--wrapper { + float: none; + padding-top: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--subcategory-column { + float: none; + width: auto; + padding: 0; + text-align: left +} + +.algolia-autocomplete .algolia-docsearch-suggestion--content { + float: none; + width: auto; + padding: 0 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--content::before { + display: none +} + +.algolia-autocomplete .ds-suggestion:not(:first-child) .algolia-docsearch-suggestion--category-header { + padding-top: .75rem; + margin-top: .75rem; + border-top: 1px solid rgba(0, 0, 0, .1) +} + +.algolia-autocomplete .ds-suggestion .algolia-docsearch-suggestion--subcategory-column { + display: block; + padding: .1rem 1rem; + margin-bottom: 0.1; + font-size: 1.0em; + font-weight: 400 + /* display: none */ +} + +.algolia-autocomplete .algolia-docsearch-suggestion--title { + display: block; + padding: .25rem 1rem; + margin-bottom: 0; + font-size: 0.9em; + font-weight: 400 +} + +.algolia-autocomplete .algolia-docsearch-suggestion--text { + padding: 0 1rem .5rem; + margin-top: -.25rem; + font-size: 0.8em; + font-weight: 400; + line-height: 1.25 +} + +.algolia-autocomplete .algolia-docsearch-footer { + width: 110px; + height: 20px; + z-index: 3; + margin-top: 10.66667px; + float: right; + font-size: 0; + line-height: 0; +} + +.algolia-autocomplete .algolia-docsearch-footer--logo { + background-image: url("data:image/svg+xml;utf8,"); + background-repeat: no-repeat; + background-position: 50%; + background-size: 100%; + overflow: hidden; + text-indent: -9000px; + width: 100%; + height: 100%; + display: block; + transform: translate(-8px); +} + +.algolia-autocomplete .algolia-docsearch-suggestion--highlight { + color: #FF8C00; + background: rgba(232, 189, 54, 0.1) +} + + +.algolia-autocomplete .algolia-docsearch-suggestion--text .algolia-docsearch-suggestion--highlight { + box-shadow: inset 0 -2px 0 0 rgba(105, 105, 105, .5) +} + +.algolia-autocomplete .ds-suggestion.ds-cursor .algolia-docsearch-suggestion--content { + background-color: rgba(192, 192, 192, .15) +} diff --git a/docs/docsearch.js b/docs/docsearch.js new file mode 100644 index 0000000..b35504c --- /dev/null +++ b/docs/docsearch.js @@ -0,0 +1,85 @@ +$(function() { + + // register a handler to move the focus to the search bar + // upon pressing shift + "/" (i.e. "?") + $(document).on('keydown', function(e) { + if (e.shiftKey && e.keyCode == 191) { + e.preventDefault(); + $("#search-input").focus(); + } + }); + + $(document).ready(function() { + // do keyword highlighting + /* modified from https://jsfiddle.net/julmot/bL6bb5oo/ */ + var mark = function() { + + var referrer = document.URL ; + var paramKey = "q" ; + + if (referrer.indexOf("?") !== -1) { + var qs = referrer.substr(referrer.indexOf('?') + 1); + var qs_noanchor = qs.split('#')[0]; + var qsa = qs_noanchor.split('&'); + var keyword = ""; + + for (var i = 0; i < qsa.length; i++) { + var currentParam = qsa[i].split('='); + + if (currentParam.length !== 2) { + continue; + } + + if (currentParam[0] == paramKey) { + keyword = decodeURIComponent(currentParam[1].replace(/\+/g, "%20")); + } + } + + if (keyword !== "") { + $(".contents").unmark({ + done: function() { + $(".contents").mark(keyword); + } + }); + } + } + }; + + mark(); + }); +}); + +/* Search term highlighting ------------------------------*/ + +function matchedWords(hit) { + var words = []; + + var hierarchy = hit._highlightResult.hierarchy; + // loop to fetch from lvl0, lvl1, etc. + for (var idx in hierarchy) { + words = words.concat(hierarchy[idx].matchedWords); + } + + var content = hit._highlightResult.content; + if (content) { + words = words.concat(content.matchedWords); + } + + // return unique words + var words_uniq = [...new Set(words)]; + return words_uniq; +} + +function updateHitURL(hit) { + + var words = matchedWords(hit); + var url = ""; + + if (hit.anchor) { + url = hit.url_without_anchor + '?q=' + escape(words.join(" ")) + '#' + hit.anchor; + } else { + url = hit.url + '?q=' + escape(words.join(" ")); + } + + return url; +} diff --git a/docs/index.html b/docs/index.html new file mode 100644 index 0000000..2a3aaf7 --- /dev/null +++ b/docs/index.html @@ -0,0 +1,198 @@ + + + + + + + +Signal Annotation Tools for High Resolution Metabolomics • mzAnnotation + + + + + + + + + + +
    +
    + + + + +
    +
    +
    +

    +mzAnnotation

    + +

    An R package containing tools for putative annotation of accurate m/z from electrospray ionisation mass spectrometry data.

    +
    +

    +Installation

    +

    To install run:

    +
    +devtools::install_github('jasenfinch/mzAnnotation')
    +
    +
    +

    +Tools

    +

    Available tools include:

    +
      +
    • Adduct, isotope and biotransfromation relationship prediction
      • +
    +
    +res <- relationshipCalculator(c(132.03023,168.00691))
+
+res
+#> # A tibble: 1 x 9
+#>   `m/z1` `m/z2` Adduct1 Adduct2 Isotope1 Isotope2 Transformation1
+#>    <dbl>  <dbl> <chr>   <chr>   <lgl>    <lgl>    <lgl>          
+#> 1   132.   168. [M-H]1- [M+Cl]… NA       NA       NA             
+#> # … with 2 more variables: Transformation2 <lgl>, Error <dbl>
    +
      +
    • Molecular formula generation
      • +
    +
    +res <- generateMF(342.11621,
+                  element_max = c(C = 12,H = 22,N = 0,
+                                O = 11,P = 0,S = 0))
+res
+#> # A tibble: 1 x 3
+#>   MF         Mass `PPM Error`
+#>   <chr>     <dbl>       <dbl>
+#> 1 C12H22O11  342.           0
    +
      +
    • Isotope distribution calculation
      • +
    +
    +res <- isotopeDistribution(MF = 'C4H5O5',charge = -1)
+res
+#> # A tibble: 8 x 4
+#>   Isotope      `m/z` `Relative Abundance` Probability
+#>   <chr>        <dbl>                <dbl>       <dbl>
+#> 1 <NA>          133.            1           0.945    
+#> 2 13C 1         134.            0.0449      0.0424   
+#> 3 18O 1         135.            0.0100      0.00947  
+#> 4 17O 1         134.            0.00200     0.00189  
+#> 5 13C 2         135.            0.000756    0.000714 
+#> 6 2H 1          134.            0.000500    0.000472 
+#> 7 13C 1; 18O 1  136.            0.000450    0.000425 
+#> 8 13C 1; 17O 1  135.            0.0000900   0.0000850
    +
      +
    • Putative ionisation product searches
      • +
    +
    +db <- metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES))
+res <- PIPsearch(db = db,
+                 mz = 132.03023,
+                 ppm = 5,
+                 adduct = '[M-H]1-',
+                 isotope = NA)
+res
+#> # A tibble: 1 x 12
+#>      ID NAME  InChI InChIKey SMILES MF    Accurate_Mass Isotope Adduct
+#>   <int> <chr> <chr> <chr>    <chr>  <chr>         <dbl> <lgl>   <chr> 
+#> 1     4 L-As… InCh… CKLJMWT… C([C@… C4H7…          133. NA      [M-H]…
+#> # … with 3 more variables: `Measured m/z` <dbl>, `Theoretical m/z` <dbl>, `PPM
+#> #   Error` <dbl>
    +
    +
    +
    + + +
    + + +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + diff --git a/docs/link.svg b/docs/link.svg new file mode 100644 index 0000000..88ad827 --- /dev/null +++ b/docs/link.svg @@ -0,0 +1,12 @@ + + + + + + diff --git a/docs/news/index.html b/docs/news/index.html new file mode 100644 index 0000000..c0a426b --- /dev/null +++ b/docs/news/index.html @@ -0,0 +1,154 @@ + + + + + + + + +Changelog • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Changelog

    + Source: NEWS.md +
    + +
    +

    +mzAnnotation 1.7.3

    + +
    +
    + + + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/pkgdown.css b/docs/pkgdown.css new file mode 100644 index 0000000..1273238 --- /dev/null +++ b/docs/pkgdown.css @@ -0,0 +1,367 @@ +/* Sticky footer */ + +/** + * Basic idea: https://philipwalton.github.io/solved-by-flexbox/demos/sticky-footer/ + * Details: https://github.com/philipwalton/solved-by-flexbox/blob/master/assets/css/components/site.css + * + * .Site -> body > .container + * .Site-content -> body > .container .row + * .footer -> footer + * + * Key idea seems to be to ensure that .container and __all its parents__ + * have height set to 100% + * + */ + +html, body { + height: 100%; +} + +body { + position: relative; +} + +body > .container { + display: flex; + height: 100%; + flex-direction: column; +} + +body > .container .row { + flex: 1 0 auto; +} + +footer { + margin-top: 45px; + padding: 35px 0 36px; + border-top: 1px solid #e5e5e5; + color: #666; + display: flex; + flex-shrink: 0; +} +footer p { + margin-bottom: 0; +} +footer div { + flex: 1; +} +footer .pkgdown { + text-align: right; +} +footer p { + margin-bottom: 0; +} + +img.icon { + float: right; +} + +img { + max-width: 100%; +} + +/* Fix bug in bootstrap (only seen in firefox) */ +summary { + display: list-item; +} + +/* Typographic tweaking ---------------------------------*/ + +.contents .page-header { + margin-top: calc(-60px + 1em); +} + +dd { + margin-left: 3em; +} + +/* Section anchors ---------------------------------*/ + +a.anchor { + margin-left: -30px; + display:inline-block; + width: 30px; + height: 30px; + visibility: hidden; + + background-image: url(./link.svg); + background-repeat: no-repeat; + background-size: 20px 20px; + background-position: center center; +} + +.hasAnchor:hover a.anchor { + visibility: visible; +} + +@media (max-width: 767px) { + .hasAnchor:hover a.anchor { + visibility: hidden; + } +} + + +/* Fixes for fixed navbar --------------------------*/ + +.contents h1, .contents h2, .contents h3, .contents h4 { + padding-top: 60px; + margin-top: -40px; +} + +/* Navbar submenu --------------------------*/ + +.dropdown-submenu { + position: relative; +} + +.dropdown-submenu>.dropdown-menu { + top: 0; + left: 100%; + margin-top: -6px; + margin-left: -1px; + border-radius: 0 6px 6px 6px; +} + +.dropdown-submenu:hover>.dropdown-menu { + display: block; +} + +.dropdown-submenu>a:after { + display: block; + content: " "; + float: right; + width: 0; + height: 0; + border-color: transparent; + border-style: solid; + border-width: 5px 0 5px 5px; + border-left-color: #cccccc; + margin-top: 5px; + margin-right: -10px; +} + +.dropdown-submenu:hover>a:after { + border-left-color: #ffffff; +} + +.dropdown-submenu.pull-left { + float: none; +} + +.dropdown-submenu.pull-left>.dropdown-menu { + left: -100%; + margin-left: 10px; + border-radius: 6px 0 6px 6px; +} + +/* Sidebar --------------------------*/ + +#pkgdown-sidebar { + margin-top: 30px; + position: -webkit-sticky; + position: sticky; + top: 70px; +} + +#pkgdown-sidebar h2 { + font-size: 1.5em; + margin-top: 1em; +} + +#pkgdown-sidebar h2:first-child { + margin-top: 0; +} + +#pkgdown-sidebar .list-unstyled li { + margin-bottom: 0.5em; +} + +/* bootstrap-toc tweaks ------------------------------------------------------*/ + +/* All levels of nav */ + +nav[data-toggle='toc'] .nav > li > a { + padding: 4px 20px 4px 6px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; +} + +nav[data-toggle='toc'] .nav > li > a:hover, +nav[data-toggle='toc'] .nav > li > a:focus { + padding-left: 5px; + color: inherit; + border-left: 1px solid #878787; +} + +nav[data-toggle='toc'] .nav > .active > a, +nav[data-toggle='toc'] .nav > .active:hover > a, +nav[data-toggle='toc'] .nav > .active:focus > a { + padding-left: 5px; + font-size: 1.5rem; + font-weight: 400; + color: inherit; + border-left: 2px solid #878787; +} + +/* Nav: second level (shown on .active) */ + +nav[data-toggle='toc'] .nav .nav { + display: none; /* Hide by default, but at >768px, show it */ + padding-bottom: 10px; +} + +nav[data-toggle='toc'] .nav .nav > li > a { + padding-left: 16px; + font-size: 1.35rem; +} + +nav[data-toggle='toc'] .nav .nav > li > a:hover, +nav[data-toggle='toc'] .nav .nav > li > a:focus { + padding-left: 15px; +} + +nav[data-toggle='toc'] .nav .nav > .active > a, +nav[data-toggle='toc'] .nav .nav > .active:hover > a, +nav[data-toggle='toc'] .nav .nav > .active:focus > a { + padding-left: 15px; + font-weight: 500; + font-size: 1.35rem; +} + +/* orcid ------------------------------------------------------------------- */ + +.orcid { + font-size: 16px; + color: #A6CE39; + /* margins are required by official ORCID trademark and display guidelines */ + margin-left:4px; + margin-right:4px; + vertical-align: middle; +} + +/* Reference index & topics ----------------------------------------------- */ + +.ref-index th {font-weight: normal;} + +.ref-index td {vertical-align: top; min-width: 100px} +.ref-index .icon {width: 40px;} +.ref-index .alias {width: 40%;} +.ref-index-icons .alias {width: calc(40% - 40px);} +.ref-index .title {width: 60%;} + +.ref-arguments th {text-align: right; padding-right: 10px;} +.ref-arguments th, .ref-arguments td {vertical-align: top; min-width: 100px} +.ref-arguments .name {width: 20%;} +.ref-arguments .desc {width: 80%;} + +/* Nice scrolling for wide elements --------------------------------------- */ + +table { + display: block; + overflow: auto; +} + +/* Syntax highlighting ---------------------------------------------------- */ + +pre { + word-wrap: normal; + word-break: normal; + border: 1px solid #eee; +} + +pre, code { + background-color: #f8f8f8; + color: #333; +} + +pre code { + overflow: auto; + word-wrap: normal; + white-space: pre; +} + +pre .img { + margin: 5px 0; +} + +pre .img img { + background-color: #fff; + display: block; + height: auto; +} + +code a, pre a { + color: #375f84; +} + +a.sourceLine:hover { + text-decoration: none; +} + +.fl {color: #1514b5;} +.fu {color: #000000;} /* function */ +.ch,.st {color: #036a07;} /* string */ +.kw {color: #264D66;} /* keyword */ +.co {color: #888888;} /* comment */ + +.message { color: black; font-weight: bolder;} +.error { color: orange; font-weight: bolder;} +.warning { color: #6A0366; font-weight: bolder;} + +/* Clipboard --------------------------*/ + +.hasCopyButton { + position: relative; +} + +.btn-copy-ex { + position: absolute; + right: 0; + top: 0; + visibility: hidden; +} + +.hasCopyButton:hover button.btn-copy-ex { + visibility: visible; +} + +/* headroom.js ------------------------ */ + +.headroom { + will-change: transform; + transition: transform 200ms linear; +} +.headroom--pinned { + transform: translateY(0%); +} +.headroom--unpinned { + transform: translateY(-100%); +} + +/* mark.js ----------------------------*/ + +mark { + background-color: rgba(255, 255, 51, 0.5); + border-bottom: 2px solid rgba(255, 153, 51, 0.3); + padding: 1px; +} + +/* vertical spacing after htmlwidgets */ +.html-widget { + margin-bottom: 10px; +} + +/* fontawesome ------------------------ */ + +.fab { + font-family: "Font Awesome 5 Brands" !important; +} + +/* don't display links in code chunks when printing */ +/* source: https://stackoverflow.com/a/10781533 */ +@media print { + code a:link:after, code a:visited:after { + content: ""; + } +} diff --git a/docs/pkgdown.js b/docs/pkgdown.js new file mode 100644 index 0000000..7e7048f --- /dev/null +++ b/docs/pkgdown.js @@ -0,0 +1,108 @@ +/* http://gregfranko.com/blog/jquery-best-practices/ */ +(function($) { + $(function() { + + $('.navbar-fixed-top').headroom(); + + $('body').css('padding-top', $('.navbar').height() + 10); + $(window).resize(function(){ + $('body').css('padding-top', $('.navbar').height() + 10); + }); + + $('[data-toggle="tooltip"]').tooltip(); + + var cur_path = paths(location.pathname); + var links = $("#navbar ul li a"); + var max_length = -1; + var pos = -1; + for (var i = 0; i < links.length; i++) { + if (links[i].getAttribute("href") === "#") + continue; + // Ignore external links + if (links[i].host !== location.host) + continue; + + var nav_path = paths(links[i].pathname); + + var length = prefix_length(nav_path, cur_path); + if (length > max_length) { + max_length = length; + pos = i; + } + } + + // Add class to parent
  • , and enclosing
  • if in dropdown + if (pos >= 0) { + var menu_anchor = $(links[pos]); + menu_anchor.parent().addClass("active"); + menu_anchor.closest("li.dropdown").addClass("active"); + } + }); + + function paths(pathname) { + var pieces = pathname.split("/"); + pieces.shift(); // always starts with / + + var end = pieces[pieces.length - 1]; + if (end === "index.html" || end === "") + pieces.pop(); + return(pieces); + } + + // Returns -1 if not found + function prefix_length(needle, haystack) { + if (needle.length > haystack.length) + return(-1); + + // Special case for length-0 haystack, since for loop won't run + if (haystack.length === 0) { + return(needle.length === 0 ? 0 : -1); + } + + for (var i = 0; i < haystack.length; i++) { + if (needle[i] != haystack[i]) + return(i); + } + + return(haystack.length); + } + + /* Clipboard --------------------------*/ + + function changeTooltipMessage(element, msg) { + var tooltipOriginalTitle=element.getAttribute('data-original-title'); + element.setAttribute('data-original-title', msg); + $(element).tooltip('show'); + element.setAttribute('data-original-title', tooltipOriginalTitle); + } + + if(ClipboardJS.isSupported()) { + $(document).ready(function() { + var copyButton = ""; + + $(".examples, div.sourceCode").addClass("hasCopyButton"); + + // Insert copy buttons: + $(copyButton).prependTo(".hasCopyButton"); + + // Initialize tooltips: + $('.btn-copy-ex').tooltip({container: 'body'}); + + // Initialize clipboard: + var clipboardBtnCopies = new ClipboardJS('[data-clipboard-copy]', { + text: function(trigger) { + return trigger.parentNode.textContent; + } + }); + + clipboardBtnCopies.on('success', function(e) { + changeTooltipMessage(e.trigger, 'Copied!'); + e.clearSelection(); + }); + + clipboardBtnCopies.on('error', function() { + changeTooltipMessage(e.trigger,'Press Ctrl+C or Command+C to copy'); + }); + }); + } +})(window.jQuery || window.$) diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml new file mode 100644 index 0000000..6d6e1a4 --- /dev/null +++ b/docs/pkgdown.yml @@ -0,0 +1,6 @@ +pandoc: 2.11.2 +pkgdown: 1.6.1 +pkgdown_sha: ~ +articles: {} +last_built: 2021-02-17T23:30Z + diff --git a/docs/reference/MetaboliteDatabase-class.html b/docs/reference/MetaboliteDatabase-class.html new file mode 100644 index 0000000..318b786 --- /dev/null +++ b/docs/reference/MetaboliteDatabase-class.html @@ -0,0 +1,153 @@ + + + + + + + + +Metabolite database class — MetaboliteDatabase-class • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Metabolite database class

    + Source: R/allClasses.R + +
    + +
    +

    Metabolite database class

    +
    + + + + +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/PIPsearch.html b/docs/reference/PIPsearch.html new file mode 100644 index 0000000..eb41c86 --- /dev/null +++ b/docs/reference/PIPsearch.html @@ -0,0 +1,211 @@ + + + + + + + + +Putative ionisation product search — PIPsearch • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Putative ionisation product search

    + Source: R/allGenerics.R, R/PIPsearch.R + +
    + +
    +

    Putative ionisation product search

    +
    + + 
    PIPsearch(
+  db,
+  mz,
+  ppm,
+  adduct,
+  isotope = NA,
+  isotopeTable = isotopes(),
+  adductTable = adducts()
+)
+
+# S4 method for MetaboliteDatabase
+PIPsearch(
+  db,
+  mz,
+  ppm,
+  adduct,
+  isotope = NA,
+  isotopeTable = isotopes(),
+  adductTable = adducts()
+)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    db

    object of class MetaboliteDatabase.

    mz

    the accurate m/z to search.

    ppm

    the parts per million threshold to search.

    adduct

    the adduct name to search.

    isotope

    the isotope name to search. Defaults to NA for non-isotopic searches.

    isotopeTable

    isotope table containing available isotope rules. Defaults to table returned by isotopes().

    adductTable

    adduct table containing available adduct rules. Defaults to table returned by adducts().

    + +

    Author

    + +

    Jasen Finch

    + +

    Examples

    + 
    res <- PIPsearch(metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES)),132.03023,5,'[M-H]1-')
+
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/Rplot001.png b/docs/reference/Rplot001.png new file mode 100644 index 0000000000000000000000000000000000000000..17a358060aed2a86950757bbd25c6f92c08c458f GIT binary patch literal 1011 zcmeAS@N?(olHy`uVBq!ia0y~yV0-|=9Be?5+AI5}0x7m6Z+90U4Fo@(ch>_c&H|6f zVg?3oArNM~bhqvg0|WD9PZ!6KiaBo&GBN^{G%5UFpXcEKVvd5*5Eu=C0SJK)8A6*F U7`aXvEC5;V>FVdQ&MBb@00SN#Z2$lO literal 0 HcmV?d00001 diff --git a/docs/reference/adductTransformMF.html b/docs/reference/adductTransformMF.html new file mode 100644 index 0000000..22380b4 --- /dev/null +++ b/docs/reference/adductTransformMF.html @@ -0,0 +1,173 @@ + + + + + + + + +Molecular formula adduct transformation — adductTransformMF • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Molecular formula adduct transformation

    + Source: R/adductTransfromMF.R + +
    + +
    +

    adduct transform a molecular formula.

    +
    + + 
    adductTransformMF(MF, adduct, Adducts = adducts())
    + +

    Arguments

    + + + + + + + + + + + + + + +
    MF

    molecular formula to transform.

    adduct

    adduct to use for transformation.

    Adducts

    Adduct information table to use. Defaults to mzAnnotation::Adducts.

    + + +

    Examples

    + 
    adductTransformMF('C6H12O6','[M+H]1+')
+
    #> [1] "C6H13O6"
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/adducts.html b/docs/reference/adducts.html new file mode 100644 index 0000000..312fa12 --- /dev/null +++ b/docs/reference/adducts.html @@ -0,0 +1,170 @@ + + + + + + + + +Adduct formation rules — adducts • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Adduct formation rules

    + Source: R/data.R + +
    + +
    +

    Formation rules for electrospray ionisation adducts

    +
    + + 
    adducts()
    + + +

    Format

    + +

    A tibble containing 58 rows and 6 columns

    +
    Name

    Adduct name

    +
    Charge

    Charge added

    +
    xM

    Number of M needed

    +
    Add

    Mass value change

    +
    Nelec

    Electron change

    +
    AddAt

    pseudo formula of the atoms to be added to the molecular formula of one M

    +
    RemAt

    pseudo formula of the atoms to be removed to the molecular formula of one M

    +
    AddEx

    pseudo formula of the atoms to be added to the final ionisation product molecular formula

    +
    RemEx

    pseudo formula of the atoms to be removed to the final ionisation product molecular formula

    +
    Rule

    Structural rule for formation

    + +
    + + +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/aminoAcids.html b/docs/reference/aminoAcids.html new file mode 100644 index 0000000..f75b61e --- /dev/null +++ b/docs/reference/aminoAcids.html @@ -0,0 +1,165 @@ + + + + + + + + +Example amino acids — aminoAcids • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Example amino acids

    + Source: R/aminoAcids.R + +
    + +
    +

    Chemical structures of the essential amino acids

    +
    + + 
    aminoAcids
    + + +

    Format

    + +

    a tibble containing 20 rows and 6 columns

    +
    ACCESSION_ID

    +
    NAME

    +
    InChi

    +
    InChiKey

    +
    SMILES

    + +
    + + +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/calcAccurateMass.html b/docs/reference/calcAccurateMass.html new file mode 100644 index 0000000..c949c32 --- /dev/null +++ b/docs/reference/calcAccurateMass.html @@ -0,0 +1,173 @@ + + + + + + + + +Calculate molecular formula accurate mass — calcAccurateMass • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Calculate molecular formula accurate mass

    + Source: R/calcAccurateMass.R + +
    + +
    +

    calculate the accurate mass of a given molecular formula

    +
    + + 
    calcAccurateMass(MF, charge = 0, elementTable = elements())
    + +

    Arguments

    + + + + + + + + + + + + + + +
    MF

    molecular formula for which to calculate the accrate mass

    charge

    charge of the given molecular formula

    elementTable

    element information table. Defaults to elements().

    + + +

    Examples

    + 
    calcAccurateMass('C4H5O5',charge = 0)
+
    #> [1] 133.0137
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/calcAdducts.html b/docs/reference/calcAdducts.html new file mode 100644 index 0000000..7768cb2 --- /dev/null +++ b/docs/reference/calcAdducts.html @@ -0,0 +1,177 @@ + + + + + + + + +Calculate adducts — calcAdducts • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Calculate adducts

    + Source: R/allGenerics.R, R/calcAdducts.R + +
    + +
    +

    Calculate ionisation products for given database accession.

    +
    + + 
    calcAdducts(db, id, adductTable = adducts())
+
+# S4 method for MetaboliteDatabase
+calcAdducts(db, id, adductTable = adducts())
    + +

    Arguments

    + + + + + + + + + + + + + + +
    db

    object of class MetaboliteDatabase

    id

    accession id

    adductTable

    table of adduct rules. Defaults to adducts()

    + + +

    Examples

    + 
    db <- metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES))
+add <- calcAdducts(db,1)
+
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/calcM.html b/docs/reference/calcM.html new file mode 100644 index 0000000..851f98c --- /dev/null +++ b/docs/reference/calcM.html @@ -0,0 +1,197 @@ + + + + + + + + +Calculate the mass of an m/z — calcM • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Calculate the mass of an m/z

    + Source: R/calcM.R + +
    + +
    +

    calculate M for a given m/z, adduct, isotope and transformation

    +
    + + 
    calcM(
+  mz,
+  adduct = "[M+H]1+",
+  isotope = NA,
+  transformation = NA,
+  adductTable = adducts(),
+  isotopeTable = isotopes(),
+  transformationTable = transformations()
+)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    mz

    m/z for which to calculate M

    adduct

    adduct to apply

    isotope

    isotope to apply

    transformation

    transformation to apply

    adductTable

    adduct table containing available adduct rules. Defaults to Adducts.

    isotopeTable

    isotope table containing available isotope rules. Defaults to Isotopes.

    transformationTable

    transformations table containing available transformations rules. Defaults to Transformations.

    + + +

    Examples

    + 
    calcM(118.08626,adduct = '[M+H]1+',isotope = '13C',transformation = 'M - [O] + NH2]')
+
    #> numeric(0)
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/calcMZ.html b/docs/reference/calcMZ.html new file mode 100644 index 0000000..1ec9aa0 --- /dev/null +++ b/docs/reference/calcMZ.html @@ -0,0 +1,197 @@ + + + + + + + + +Calculate the m/z of a mass — calcMZ • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Calculate the m/z of a mass

    + Source: R/calcMZ.R + +
    + +
    +

    calculate an m/z for a given M, adduct, isotope and transformation

    +
    + + 
    calcMZ(
+  M,
+  adduct = "[M+H]1+",
+  isotope = NA,
+  transformation = NA,
+  adductTable = adducts(),
+  isotopeTable = isotopes(),
+  transformationTable = transformations()
+)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    M

    M for which to calculate an m/z

    adduct

    adduct to apply

    isotope

    isotope to apply

    transformation

    transformation to apply

    adductTable

    adduct table containing available adduct rules. Defaults to adducts().

    isotopeTable

    isotope table containing available isotope rules. Defaults to isotopes().

    transformationTable

    transformations table containing available transformations rules. Defaults to transformations().

    + + +

    Examples

    + 
    calcMZ(116.05182,adduct = '[M+H]1+',isotope = '13C',transformation = 'M - [O] + NH2]')
+
    #> numeric(0)
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/convert.html b/docs/reference/convert.html new file mode 100644 index 0000000..c310a11 --- /dev/null +++ b/docs/reference/convert.html @@ -0,0 +1,173 @@ + + + + + + + + +Convert chemical notation — convert • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Convert chemical notation

    + Source: R/convert.R + +
    + +
    +

    convert between SMILES and Inchi and to InchiKey

    +
    + + 
    convert(input, inputType, outputType)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    input

    a valid SMILE or Inchi

    inputType

    either "smiles" or "inchi", denoting the input type

    outputType

    either "smiles", "inchi" or "inchikey", denoting the output type

    + + +

    Examples

    + 
    convert(aminoAcids$SMILES[1],'smiles','inchi')
+
    #> [1] "InChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m0/s1"
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/descriptors.html b/docs/reference/descriptors.html new file mode 100644 index 0000000..c68b23f --- /dev/null +++ b/docs/reference/descriptors.html @@ -0,0 +1,190 @@ + + + + + + + + +Molecular descriptors — descriptors • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Molecular descriptors

    + Source: R/descriptors.R + +
    + +
    +

    Molecular descriptors

    +
    + + 
    descriptors(SMILES)
    + +

    Arguments

    + + + + + + +
    SMILES

    a character vector of valid SMILES

    + + +

    Examples

    + 
    data(aminoAcids)
+descriptors(aminoAcids$SMILES)
+
    #> # A tibble: 20 x 15
+#>    SMILES MF    Accurate_Mass Negative_Charge Positive_Charge Total_Charge  HBA1
+#>    <chr>  <chr>         <dbl>           <int>           <int>        <int> <dbl>
+#>  1 C[C@@… C3H7…          89.0               0               0            0     3
+#>  2 C(C[C… C6H1…         174.                0               0            0     6
+#>  3 C([C@… C4H8…         132.                0               0            0     5
+#>  4 C([C@… C4H7…         133.                0               0            0     5
+#>  5 C([C@… C3H7…         121.                0               0            0     4
+#>  6 C(CC(… C5H9…         147.                0               0            0     5
+#>  7 C(CC(… C5H1…         146.                0               0            0     5
+#>  8 C(C(=… C2H5…          75.0               0               0            0     3
+#>  9 C(c1c… C6H9…         155.                0               0            0     4
+#> 10 CC[C@… C6H1…         131.                0               0            0     3
+#> 11 CC(C)… C6H1…         131.                0               0            0     3
+#> 12 C(CCN… C6H1…         146.                0               0            0     4
+#> 13 CSCC[… C5H1…         149.                0               0            0     4
+#> 14 c1ccc… C9H1…         165.                0               0            0     3
+#> 15 C1C[C… C5H9…         115.                0               0            0     3
+#> 16 C([C@… C3H7…         105.                0               0            0     4
+#> 17 C[C@H… C4H9…         119.                0               0            0     4
+#> 18 c1ccc… C11H…         204.                0               0            0     3
+#> 19 c1cc(… C9H1…         181.                0               0            0     4
+#> 20 CC(C)… C5H1…         117.                0               0            0     3
+#> # … with 8 more variables: HBA2 <dbl>, HBD <dbl>, logP <dbl>, TPSA <dbl>,
+#> #   NHH <int>, OH <int>, COOH <int>, COO <int>
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/elements.html b/docs/reference/elements.html new file mode 100644 index 0000000..f8926cd --- /dev/null +++ b/docs/reference/elements.html @@ -0,0 +1,157 @@ + + + + + + + + +Elemental information — elements • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Elemental information

    + Source: R/data.R + +
    + +
    +

    Elemental information

    +
    + + 
    elements()
    + + +

    Format

    + +

    A tibble containing 31 rows and 5 columns.

    + +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/filterACCESSIONS.html b/docs/reference/filterACCESSIONS.html new file mode 100644 index 0000000..bf184f5 --- /dev/null +++ b/docs/reference/filterACCESSIONS.html @@ -0,0 +1,173 @@ + + + + + + + + +Filter accessions — filterACCESSIONS • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Filter accessions

    + Source: R/allGenerics.R, R/filter-methods.R + +
    + +
    +

    Filter a MetaboliteDatabase based on given accession IDs.

    +
    + + 
    filterACCESSIONS(db, ids)
+
+# S4 method for MetaboliteDatabase
+filterACCESSIONS(db, ids)
    + +

    Arguments

    + + + + + + + + + + +
    db

    S4 object of class MetaboliteDatabase

    ids

    vector of accession IDs

    + + +

    Examples

    + 
    db <- metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES))
+db <- filterACCESSIONS(db,c(1,2))
+
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/filterER.html b/docs/reference/filterER.html new file mode 100644 index 0000000..347f46e --- /dev/null +++ b/docs/reference/filterER.html @@ -0,0 +1,173 @@ + + + + + + + + +Filter using an elemental rule — filterER • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Filter using an elemental rule

    + Source: R/allGenerics.R, R/filter-methods.R + +
    + +
    +

    Filter a MetaboliteDatabase based on an elemental rule.

    +
    + + 
    filterER(db, rule)
+
+# S4 method for MetaboliteDatabase
+filterER(db, rule)
    + +

    Arguments

    + + + + + + + + + + +
    db

    S4 object of class MetaboliteDatabase

    rule

    elemental rule given as a string

    + + +

    Examples

    + 
    db <- metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES))
+db <- filterER(db,'S>0')
+
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/filterIP.html b/docs/reference/filterIP.html new file mode 100644 index 0000000..ea2943a --- /dev/null +++ b/docs/reference/filterIP.html @@ -0,0 +1,174 @@ + + + + + + + + +Filter using an ionisation rule — filterIP • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Filter using an ionisation rule

    + Source: R/allGenerics.R, R/filter-methods.R + +
    + +
    +

    Filter MetaboliteDatabase based on an ionisation rule

    +
    + + 
    filterIP(db, rule)
+
+# S4 method for MetaboliteDatabase
+filterIP(db, rule)
    + +

    Arguments

    + + + + + + + + + + +
    db

    S4 object of class MetaboliteDatabase

    rule

    Character containing ionisation rule.

    + + +

    Examples

    + 
    rule <- adducts()$Rule[52]
+db <- metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES))
+db <- filterIP(db,rule)
+
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/filterMF.html b/docs/reference/filterMF.html new file mode 100644 index 0000000..4c0ea61 --- /dev/null +++ b/docs/reference/filterMF.html @@ -0,0 +1,173 @@ + + + + + + + + +Filter a molecular formula — filterMF • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Filter a molecular formula

    + Source: R/allGenerics.R, R/filter-methods.R + +
    + +
    +

    Filter a MetaboliteDatabase based on given molecular formulas

    +
    + + 
    filterMF(db, mf)
+
+# S4 method for MetaboliteDatabase
+filterMF(db, mf)
    + +

    Arguments

    + + + + + + + + + + +
    db

    S4 object of class MetaboliteDatabase

    mf

    character vector of molecular formulas

    + + +

    Examples

    + 
    db <- metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES))
+db <- filterMF(db,c('C3H7NO2','C5H10N2O3'))
+
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/filterMR.html b/docs/reference/filterMR.html new file mode 100644 index 0000000..14d2a3a --- /dev/null +++ b/docs/reference/filterMR.html @@ -0,0 +1,177 @@ + + + + + + + + +Filter a mass range — filterMR • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Filter a mass range

    + Source: R/allGenerics.R, R/filter-methods.R + +
    + +
    +

    Filter a MetaboliteDatabase for a given mass range.

    +
    + + 
    filterMR(db, lower, upper)
+
+# S4 method for MetaboliteDatabase
+filterMR(db, lower, upper)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    db

    S4 object of class MetaboliteDatabase

    lower

    lower mass boundary

    upper

    upper mass boundary

    + + +

    Examples

    + 
    db <- metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES))
+db <- filterMR(db,100,120)
+
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/generateMF.html b/docs/reference/generateMF.html new file mode 100644 index 0000000..6718e9d --- /dev/null +++ b/docs/reference/generateMF.html @@ -0,0 +1,203 @@ + + + + + + + + +Molecular formula generation — generateMF • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Molecular formula generation

    + Source: R/generateMF.R + +
    + +
    +

    Molecular formula generation

    +
    + + 
    generateMF(
+  mass,
+  ppm = 1,
+  charge = 0,
+  validation = TRUE,
+  element_max = c(C = 12, H = 22, N = 0, O = 11, P = 0, S = 0),
+  element_min = c(C = 0, H = 0, N = 0, O = 0, P = 0, S = 0)
+)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + +
    mass

    accurate mass

    ppm

    ppm tolerance

    charge

    charge

    validation

    boolean, apply validation rules

    element_max

    numeric vector of maximum elemental composition

    element_min

    numeric vector of minimum elemental composition

    + +

    Value

    + +

    A tibble containing the generated MFs, their theoretical mass and their PPM error.

    +

    Details

    + +

    this uses the HR2 molecular formula generator available at http://maltese.dbs.aber.ac.uk:8888/hrmet/supp/rhrmet.html.

    +

    Author

    + +

    Jasen Finch

    + +

    Examples

    + 
    res <- generateMF(342.11621,
+                  element_max = c(C = 12,H = 22,N = 0,
+                                O = 11,P = 0,S = 0))
+
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/getAccessions.html b/docs/reference/getAccessions.html new file mode 100644 index 0000000..6382dc4 --- /dev/null +++ b/docs/reference/getAccessions.html @@ -0,0 +1,165 @@ + + + + + + + + +Retrieve accessions — getAccessions • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Retrieve accessions

    + Source: R/allGenerics.R, R/get-methods.R + +
    + +
    +

    return accession data table from MetaboliteDatabase object

    +
    + + 
    getAccessions(db)
+
+# S4 method for MetaboliteDatabase
+getAccessions(db)
    + +

    Arguments

    + + + + + + +
    db

    MetaboliteDatabase

    + + +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/getDescriptors.html b/docs/reference/getDescriptors.html new file mode 100644 index 0000000..776cab9 --- /dev/null +++ b/docs/reference/getDescriptors.html @@ -0,0 +1,165 @@ + + + + + + + + +Retrieve descriptors — getDescriptors • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Retrieve descriptors

    + Source: R/allGenerics.R, R/get-methods.R + +
    + +
    +

    return descriptor data table from MetaboliteDatabase object

    +
    + + 
    getDescriptors(db)
+
+# S4 method for MetaboliteDatabase
+getDescriptors(db)
    + +

    Arguments

    + + + + + + +
    db

    MetaboliteDatabase

    + + +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/index.html b/docs/reference/index.html new file mode 100644 index 0000000..ee631b6 --- /dev/null +++ b/docs/reference/index.html @@ -0,0 +1,365 @@ + + + + + + + + +Function reference • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Reference

    +
    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +

    All functions

    +

    +
    +

    MetaboliteDatabase-class

    +

    Metabolite database class

    +

    PIPsearch()

    +

    Putative ionisation product search

    +

    adductTransformMF()

    +

    Molecular formula adduct transformation

    +

    adducts()

    +

    Adduct formation rules

    +

    aminoAcids

    +

    Example amino acids

    +

    calcAccurateMass()

    +

    Calculate molecular formula accurate mass

    +

    calcAdducts()

    +

    Calculate adducts

    +

    calcM()

    +

    Calculate the mass of an m/z

    +

    calcMZ()

    +

    Calculate the m/z of a mass

    +

    convert()

    +

    Convert chemical notation

    +

    descriptors()

    +

    Molecular descriptors

    +

    elements()

    +

    Elemental information

    +

    filterACCESSIONS()

    +

    Filter accessions

    +

    filterER()

    +

    Filter using an elemental rule

    +

    filterIP()

    +

    Filter using an ionisation rule

    +

    filterMF()

    +

    Filter a molecular formula

    +

    filterMR()

    +

    Filter a mass range

    +

    generateMF()

    +

    Molecular formula generation

    +

    getAccessions()

    +

    Retrieve accessions

    +

    getDescriptors()

    +

    Retrieve descriptors

    +

    ionisationProducts()

    +

    Ionisation products

    +

    isotopeDistribution()

    +

    Isotopic distribution calculator

    +

    isotopes()

    +

    Isotopic rules

    +

    metaboliteDB()

    +

    Create a metabolite database

    +

    ppmError()

    +

    Calculate PPM error

    +

    ppmRange()

    +

    Calculate a PPM error range

    +

    relationshipCalculator()

    +

    m/z relationship calculation

    +

    show(<MetaboliteDatabase>)

    +

    show-MetaboliteDatabase

    +

    smartsSearch()

    +

    SMARTS substructure search

    +

    smileToAccurateMass()

    +

    Convert SMILES to accurate mass

    +

    smileToMF()

    +

    Convert SMILES to molecular formula

    +

    transformMF()

    +

    Transform a molecular formula

    +

    transformations()

    +

    Transformation rules

    +
    + + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/ionisationProducts.html b/docs/reference/ionisationProducts.html new file mode 100644 index 0000000..19699c2 --- /dev/null +++ b/docs/reference/ionisationProducts.html @@ -0,0 +1,182 @@ + + + + + + + + +Ionisation products — ionisationProducts • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Ionisation products

    + Source: R/ionisationProducts.R + +
    + +
    +

    Calculate ionisation products for a given SMILES.

    +
    + + 
    ionisationProducts(SMILES, adductTable = adducts())
    + +

    Arguments

    + + + + + + + + + + +
    SMILES

    a valid SMILES string

    adductTable

    table of adduct rules. Defaults to adducts()

    + + +

    Examples

    + 
    ionisationProducts(aminoAcids$SMILES[1])
+
    #> # A tibble: 58 x 4
+#>    Adduct         `m/z` MF         Possible
+#>    <chr>          <dbl> <chr>      <lgl>   
+#>  1 [M+3Na]3+       52.7 C3H7NNa3O2 TRUE    
+#>  2 [M+H+2Na]3+     45.3 C3H8NNa2O2 TRUE    
+#>  3 [M+2H+Na]3+     38.0 C3H9NNaO2  TRUE    
+#>  4 [M+3H]3+        30.7 C3H10NO2   TRUE    
+#>  5 [2M+3H2O+2H]2+ 117.  C6H22N2O7  TRUE    
+#>  6 [M+3ACN+2H]2+  107.  C9H18N4O2  TRUE    
+#>  7 [M+2ACN+2H]2+   86.6 C7H15N3O2  TRUE    
+#>  8 [M+2Na]2+       67.5 C3H7NNa2O2 TRUE    
+#>  9 [M+ACN+2H]2+    66.0 C5H12N2O2  TRUE    
+#> 10 [M+H+K]2+       64.5 C3H8KNO2   TRUE    
+#> # … with 48 more rows
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/isotopeDistribution.html b/docs/reference/isotopeDistribution.html new file mode 100644 index 0000000..b127931 --- /dev/null +++ b/docs/reference/isotopeDistribution.html @@ -0,0 +1,180 @@ + + + + + + + + +Isotopic distribution calculator — isotopeDistribution • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Isotopic distribution calculator

    + Source: R/isotopeDistribution.R + +
    + +
    +

    Isotopic distribution calculator

    +
    + + 
    isotopeDistribution(MF, charge, limit = 9e-05, elementTable = elements())
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + +
    MF

    the molecular formular to generate the isotope distribution

    charge

    the charge of the molecular formula

    limit

    the relative abundance threshold

    elementTable

    the table containing elemental information. Defaults to Elements.

    + +

    Author

    + +

    Jasen Finch

    + +

    Examples

    + 
    res <- isotopeDistribution('C4H5O5',charge = -1)
+
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/isotopes.html b/docs/reference/isotopes.html new file mode 100644 index 0000000..65db35d --- /dev/null +++ b/docs/reference/isotopes.html @@ -0,0 +1,163 @@ + + + + + + + + +Isotopic rules — isotopes • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Isotopic rules

    + Source: R/data.R + +
    + +
    +

    Isotope rules

    +
    + + 
    isotopes()
    + + +

    Format

    + +

    A tibble containing 8 rows and 3 columns.

    +
    Isotope

    Isotope name

    +
    Mass Difference

    Isotopic mass difference

    +
    Rule

    Elemental composition rules

    + +
    + + +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/metaboliteDB.html b/docs/reference/metaboliteDB.html new file mode 100644 index 0000000..02b98fc --- /dev/null +++ b/docs/reference/metaboliteDB.html @@ -0,0 +1,177 @@ + + + + + + + + +Create a metabolite database — metaboliteDB • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Create a metabolite database

    + Source: R/metaboliteDB.R + +
    + +
    +

    Build a metabolite database ready for use.

    +
    + + 
    metaboliteDB(accessions, descriptors, connection = NULL, type = "local")
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + +
    accessions

    tibble containing accession information. If type = 'remote' this should be the name of the table containing the accession information within the SQL database.

    descriptors

    tibble containing descriptor information as returned by descriptors(). If type = 'remote' this should be the name of the table containing the descriptor information within the SQL database.

    connection

    If type = 'remote' this should be a valid database connection as returned by DBI::dbconnect().

    type

    set to either 'local' for in-memory databases or remote for SQL database connections.

    + + +

    Examples

    + 
    db <- metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES))
+
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/mzAnnotation.html b/docs/reference/mzAnnotation.html new file mode 100644 index 0000000..9f83f34 --- /dev/null +++ b/docs/reference/mzAnnotation.html @@ -0,0 +1,153 @@ + + + + + + + + +mzAnnotation — mzAnnotation • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    mzAnnotation

    + Source: R/mzAnnotation.R + +
    + +
    +

    mzAnnotation

    +
    + + + + +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/ppmError.html b/docs/reference/ppmError.html new file mode 100644 index 0000000..70e8d07 --- /dev/null +++ b/docs/reference/ppmError.html @@ -0,0 +1,169 @@ + + + + + + + + +Calculate PPM error — ppmError • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Calculate PPM error

    + Source: R/ppmError.R + +
    + +
    +

    Calculate ppmError between a measured and theoretical m/z

    +
    + + 
    ppmError(measured, theoretical)
    + +

    Arguments

    + + + + + + + + + + +
    measured

    measured m/z

    theoretical

    theoretical m/z

    + + +

    Examples

    + 
    ppmError(118.08626,118.08647)
+
    #> [1] -1.778358
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/ppmRange.html b/docs/reference/ppmRange.html new file mode 100644 index 0000000..a17b8a8 --- /dev/null +++ b/docs/reference/ppmRange.html @@ -0,0 +1,174 @@ + + + + + + + + +Calculate a PPM error range — ppmRange • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Calculate a PPM error range

    + Source: R/RcppExports.R + +
    + +
    +

    Calculate the upper and lower ppm boundaries for a given m/z

    +
    + + 
    ppmRange(mz, ppm)
    + +

    Arguments

    + + + + + + + + + + +
    mz

    the m/z for which to calculate the range

    ppm

    the ppm

    + + +

    Examples

    + 
    ppmRange(118.08626,5)
+
    #> $lower
+#> [1] 118.0857
+#> 
+#> $upper
+#> [1] 118.0868
+#>
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/relationshipCalculator.html b/docs/reference/relationshipCalculator.html new file mode 100644 index 0000000..57a9eb1 --- /dev/null +++ b/docs/reference/relationshipCalculator.html @@ -0,0 +1,224 @@ + + + + + + + + +m/z relationship calculation — relationshipCalculator • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    m/z relationship calculation

    + Source: R/relationshipCalculator.R + +
    + +
    +

    adduct, isotope and biotransfromation calculation.

    +
    + + 
    relationshipCalculator(
+  mz,
+  limit = 0.001,
+  modes = NULL,
+  adducts = c("[M-H]1-", "[M+Cl]1-", "[M+K-2H]1-"),
+  isotopes = NULL,
+  transformations = NULL,
+  adductTable = adducts(),
+  isotopeTable = isotopes(),
+  transformationTable = transformations()
+)
    + +

    Arguments

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    mz

    numeric vector of accurate m/z

    limit

    limit of deviation for thresholding associations. Defaults to 0.001

    modes

    character vector of ionisation modes of input mz

    adducts

    character vector of adducts to use. If NULL all available adducts will be used. If modes is not NULL, this should be named list, the names denoting the adduct aquisition modes.

    isotopes

    character vector of isotopes to use.

    transformations

    character vector of transformations to use

    adductTable

    table containing adduct formation rules. Defaults to adducts().

    isotopeTable

    table containing isotope rules. Defaults to isotopes().

    transformationTable

    table containing transformation rules. Defaults to transformations().

    + +

    Author

    + +

    Jasen Finch

    + +

    Examples

    + 
    relationshipCalculator(c(132.03023,168.00691))
+
    #> # A tibble: 1 x 9
+#>   `m/z1` `m/z2` Adduct1 Adduct2 Isotope1 Isotope2 Transformation1
+#>    <dbl>  <dbl> <chr>   <chr>   <lgl>    <lgl>    <lgl>          
+#> 1   132.   168. [M-H]1- [M+Cl]… NA       NA       NA             
+#> # … with 2 more variables: Transformation2 <lgl>, Error <dbl>
    
+## with modes declared
+relationshipCalculator(c(132.03023,172.00067),
+                      modes = c('n','p'),
+                      adducts = list(n = c("[M-H]1-","[M+Cl]1-","[M+K-2H]1-"), 
+                                     p = c('[M+H]1+','[M+K]1+','[M+Na]1+')))
+
    #> # A tibble: 1 x 9
+#>   `m/z1` `m/z2` Adduct1 Adduct2 Isotope1 Isotope2 Transformation1
+#>    <dbl>  <dbl> <chr>   <chr>   <lgl>    <lgl>    <lgl>          
+#> 1   132.   172. [M-H]1- [M+K]1+ NA       NA       NA             
+#> # … with 2 more variables: Transformation2 <lgl>, Error <dbl>
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/show-MetaboliteDatabase-method.html b/docs/reference/show-MetaboliteDatabase-method.html new file mode 100644 index 0000000..0ae0015 --- /dev/null +++ b/docs/reference/show-MetaboliteDatabase-method.html @@ -0,0 +1,163 @@ + + + + + + + + +show-MetaboliteDatabase — show,MetaboliteDatabase-method • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    show-MetaboliteDatabase

    + Source: R/show-method.R + +
    + +
    +

    show method for MetaboliteDatabase class.

    +
    + + 
    # S4 method for MetaboliteDatabase
+show(object)
    + +

    Arguments

    + + + + + + +
    object

    S4 object of class MetaboliteDatabase

    + + +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/smartsSearch.html b/docs/reference/smartsSearch.html new file mode 100644 index 0000000..57e1b8a --- /dev/null +++ b/docs/reference/smartsSearch.html @@ -0,0 +1,169 @@ + + + + + + + + +SMARTS substructure search — smartsSearch • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    SMARTS substructure search

    + Source: R/RcppExports.R + +
    + +
    +

    SMARTS substructure searching for SMILES.

    +
    + + 
    smartsSearch(smile, smart)
    + +

    Arguments

    + + + + + + + + + + +
    smile

    a valid SMILE

    smart

    a valid SMARTS symbol

    + + +

    Examples

    + 
    smartsSearch(aminoAcids$SMILES[1],"[OX2H]")
+
    #> [1] 1
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/smileToAccurateMass.html b/docs/reference/smileToAccurateMass.html new file mode 100644 index 0000000..fb75e4f --- /dev/null +++ b/docs/reference/smileToAccurateMass.html @@ -0,0 +1,165 @@ + + + + + + + + +Convert SMILES to accurate mass — smileToAccurateMass • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Convert SMILES to accurate mass

    + Source: R/RcppExports.R + +
    + +
    +

    convert a smile to an accurate mass

    +
    + + 
    smileToAccurateMass(smile)
    + +

    Arguments

    + + + + + + +
    smile

    a valid SMILE

    + + +

    Examples

    + 
    smileToAccurateMass(aminoAcids$SMILES[1])
+
    #> [1] 89.04768
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/smileToMF.html b/docs/reference/smileToMF.html new file mode 100644 index 0000000..48076e5 --- /dev/null +++ b/docs/reference/smileToMF.html @@ -0,0 +1,165 @@ + + + + + + + + +Convert SMILES to molecular formula — smileToMF • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Convert SMILES to molecular formula

    + Source: R/RcppExports.R + +
    + +
    +

    convert a smile to a molecular formula

    +
    + + 
    smileToMF(smile)
    + +

    Arguments

    + + + + + + +
    smile

    a valid SMILE

    + + +

    Examples

    + 
    smileToMF(aminoAcids$SMILES[1])
+
    #> [1] "C3H7NO2"
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/transformMF.html b/docs/reference/transformMF.html new file mode 100644 index 0000000..29995b2 --- /dev/null +++ b/docs/reference/transformMF.html @@ -0,0 +1,181 @@ + + + + + + + + +Transform a molecular formula — transformMF • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Transform a molecular formula

    + Source: R/transformMF.R + +
    + +
    +

    transform a molecular formula

    +
    + + 
    transformMF(
+  MF,
+  transformation = "M - [O] + [NH2]",
+  transformationTable = transformations()
+)
    + +

    Arguments

    + + + + + + + + + + + + + + +
    MF

    molecular formula to transform

    transformation

    transformation to apply

    transformationTable

    transformations table containing available transformations rules. Defaults to Transformations.

    + +

    Details

    + +

    NA will be returned if MF cannot be transformed.

    + +

    Examples

    + 
    transformMF('C4H5O5')
+
    #> [1] "C4H7NO4"
    transformMF('C4H5N',transformation = 'M - [OH] + [NH2]')
+
    #> [1] NA
    +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/docs/reference/transformations.html b/docs/reference/transformations.html new file mode 100644 index 0000000..06f17e0 --- /dev/null +++ b/docs/reference/transformations.html @@ -0,0 +1,169 @@ + + + + + + + + +Transformation rules — transformations • mzAnnotation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + + + + +
    + +
    +
    +
    +

    Transformation rules

    + Source: R/data.R + +
    + +
    +

    Transformation rules

    +
    + + 
    transformations()
    + + +

    Format

    + +

    A tibble containing 12 rows and 9 columns.

    +
    Name

    Transformation name

    +
    MF Change

    Molecular formula change

    +
    Difference

    Mass difference

    +
    C

    Change in carbon atoms

    +
    H

    Change in hydrogen atoms

    +
    O

    Change in oxygen atoms

    +
    N

    Change in nitrogen atoms

    +
    P

    Change in phosphorus atoms

    +
    S

    Change in sulphur atoms

    + +
    + + +
    + +
    + + +
    +
    +

    Developed by Jasen Finch.

    +
    + +
    +

    Site built with pkgdown 1.6.1.

    +
    + +
    +
    + + + + + + + + diff --git a/man/MetaboliteDatabase-class.Rd b/man/MetaboliteDatabase-class.Rd index 84e9a20..f2c8061 100644 --- a/man/MetaboliteDatabase-class.Rd +++ b/man/MetaboliteDatabase-class.Rd @@ -3,7 +3,7 @@ \docType{class} \name{MetaboliteDatabase-class} \alias{MetaboliteDatabase-class} -\title{MetaboliteDatabase} +\title{Metabolite database class} \description{ -MetaboliteDatabase +Metabolite database class } diff --git a/man/PIPsearch.Rd b/man/PIPsearch.Rd index 283793e..af48966 100644 --- a/man/PIPsearch.Rd +++ b/man/PIPsearch.Rd @@ -3,7 +3,7 @@ \name{PIPsearch} \alias{PIPsearch} \alias{PIPsearch,MetaboliteDatabase-method} -\title{Putative Ionisation Product searching} +\title{Putative ionisation product search} \usage{ PIPsearch( db, @@ -41,7 +41,7 @@ PIPsearch( \item{adductTable}{adduct table containing available adduct rules. Defaults to table returned by \code{adducts()}.} } \description{ -Putative Ionisation Product searching +Putative ionisation product search } \examples{ res <- PIPsearch(metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES)),132.03023,5,'[M-H]1-') diff --git a/man/adductTransformMF.Rd b/man/adductTransformMF.Rd index 68a8a01..df9c949 100644 --- a/man/adductTransformMF.Rd +++ b/man/adductTransformMF.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/adductTransfromMF.R \name{adductTransformMF} \alias{adductTransformMF} -\title{adductTransformMF} +\title{Molecular formula adduct transformation} \usage{ adductTransformMF(MF, adduct, Adducts = adducts()) } diff --git a/man/adducts.Rd b/man/adducts.Rd index 8906057..928a899 100644 --- a/man/adducts.Rd +++ b/man/adducts.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/data.R \name{adducts} \alias{adducts} -\title{adducts} +\title{Adduct formation rules} \format{ A tibble containing 58 rows and 6 columns \describe{ diff --git a/man/aminoAcids.Rd b/man/aminoAcids.Rd index a8366d1..bd22ef5 100644 --- a/man/aminoAcids.Rd +++ b/man/aminoAcids.Rd @@ -3,7 +3,7 @@ \docType{data} \name{aminoAcids} \alias{aminoAcids} -\title{aminoAcids} +\title{Example amino acids} \format{ a tibble containing 20 rows and 6 columns \describe{ diff --git a/man/calcAccurateMass.Rd b/man/calcAccurateMass.Rd index e4ddc9b..9a5553a 100644 --- a/man/calcAccurateMass.Rd +++ b/man/calcAccurateMass.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/calcAccurateMass.R \name{calcAccurateMass} \alias{calcAccurateMass} -\title{calcAccurateMass} +\title{Calculate molecular formula accurate mass} \usage{ calcAccurateMass(MF, charge = 0, elementTable = elements()) } diff --git a/man/calcAdducts.Rd b/man/calcAdducts.Rd index e7c01fd..cc84f97 100644 --- a/man/calcAdducts.Rd +++ b/man/calcAdducts.Rd @@ -3,7 +3,7 @@ \name{calcAdducts} \alias{calcAdducts} \alias{calcAdducts,MetaboliteDatabase-method} -\title{calcAdducts} +\title{Calculate adducts} \usage{ calcAdducts(db, id, adductTable = adducts()) diff --git a/man/calcM.Rd b/man/calcM.Rd index 3ca5ae6..fff2651 100644 --- a/man/calcM.Rd +++ b/man/calcM.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/calcM.R \name{calcM} \alias{calcM} -\title{calcM} +\title{Calculate the mass of an m/z} \usage{ calcM( mz, diff --git a/man/calcMZ.Rd b/man/calcMZ.Rd index 37cb170..16fbde1 100644 --- a/man/calcMZ.Rd +++ b/man/calcMZ.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/calcMZ.R \name{calcMZ} \alias{calcMZ} -\title{calcM} +\title{Calculate the m/z of a mass} \usage{ calcMZ( M, diff --git a/man/convert.Rd b/man/convert.Rd index da1316d..d3cb6d2 100644 --- a/man/convert.Rd +++ b/man/convert.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/convert.R \name{convert} \alias{convert} -\title{convert} +\title{Convert chemical notation} \usage{ convert(input, inputType, outputType) } diff --git a/man/descriptors.Rd b/man/descriptors.Rd index fe0e7d5..00dbe03 100644 --- a/man/descriptors.Rd +++ b/man/descriptors.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/descriptors.R \name{descriptors} \alias{descriptors} -\title{convert SMILES to a series of molecular descriptors} +\title{Molecular descriptors} \usage{ descriptors(SMILES) } @@ -10,7 +10,7 @@ descriptors(SMILES) \item{SMILES}{a character vector of valid SMILES} } \description{ -convert SMILES to a series of molecular descriptors +Molecular descriptors } \examples{ data(aminoAcids) diff --git a/man/elements.Rd b/man/elements.Rd index 89a2d8a..18e0553 100644 --- a/man/elements.Rd +++ b/man/elements.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/data.R \name{elements} \alias{elements} -\title{elements} +\title{Elemental information} \format{ A tibble containing 31 rows and 5 columns. } diff --git a/man/filterACCESSIONS.Rd b/man/filterACCESSIONS.Rd index 68d89a8..7ff66fb 100644 --- a/man/filterACCESSIONS.Rd +++ b/man/filterACCESSIONS.Rd @@ -3,7 +3,7 @@ \name{filterACCESSIONS} \alias{filterACCESSIONS} \alias{filterACCESSIONS,MetaboliteDatabase-method} -\title{filterACCESSIONS} +\title{Filter accessions} \usage{ filterACCESSIONS(db, ids) diff --git a/man/filterER.Rd b/man/filterER.Rd index 519bb60..ad4fbc1 100644 --- a/man/filterER.Rd +++ b/man/filterER.Rd @@ -3,7 +3,7 @@ \name{filterER} \alias{filterER} \alias{filterER,MetaboliteDatabase-method} -\title{filterER} +\title{Filter using an elemental rule} \usage{ filterER(db, rule) diff --git a/man/filterIP.Rd b/man/filterIP.Rd index 124db8c..44a1248 100644 --- a/man/filterIP.Rd +++ b/man/filterIP.Rd @@ -3,7 +3,7 @@ \name{filterIP} \alias{filterIP} \alias{filterIP,MetaboliteDatabase-method} -\title{filterIP} +\title{Filter using an ionisation rule} \usage{ filterIP(db, rule) diff --git a/man/filterMF.Rd b/man/filterMF.Rd index e1eea32..ce64032 100644 --- a/man/filterMF.Rd +++ b/man/filterMF.Rd @@ -3,7 +3,7 @@ \name{filterMF} \alias{filterMF} \alias{filterMF,MetaboliteDatabase-method} -\title{filterMF} +\title{Filter a molecular formula} \usage{ filterMF(db, mf) diff --git a/man/filterMR.Rd b/man/filterMR.Rd index d2eccd6..d419b32 100644 --- a/man/filterMR.Rd +++ b/man/filterMR.Rd @@ -3,7 +3,7 @@ \name{filterMR} \alias{filterMR} \alias{filterMR,MetaboliteDatabase-method} -\title{filterMR} +\title{Filter a mass range} \usage{ filterMR(db, lower, upper) diff --git a/man/generateMF.Rd b/man/generateMF.Rd index ddf7d77..c513f57 100644 --- a/man/generateMF.Rd +++ b/man/generateMF.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/generateMF.R \name{generateMF} \alias{generateMF} -\title{generateMF} +\title{Molecular formula generation} \usage{ generateMF( mass, diff --git a/man/getAccessions.Rd b/man/getAccessions.Rd index 8897c66..c085b0c 100644 --- a/man/getAccessions.Rd +++ b/man/getAccessions.Rd @@ -3,7 +3,7 @@ \name{getAccessions} \alias{getAccessions} \alias{getAccessions,MetaboliteDatabase-method} -\title{getAccessions-MetaboliteDatabase} +\title{Retrieve accessions} \usage{ getAccessions(db) diff --git a/man/getDescriptors.Rd b/man/getDescriptors.Rd index 21eeaa6..a9e1bc2 100644 --- a/man/getDescriptors.Rd +++ b/man/getDescriptors.Rd @@ -3,7 +3,7 @@ \name{getDescriptors} \alias{getDescriptors} \alias{getDescriptors,MetaboliteDatabase-method} -\title{getDescriptors-MetaboliteDatabase} +\title{Retrieve descriptors} \usage{ getDescriptors(db) diff --git a/man/ionisationProducts.Rd b/man/ionisationProducts.Rd index 6cdd0c1..3c0293f 100644 --- a/man/ionisationProducts.Rd +++ b/man/ionisationProducts.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/ionisationProducts.R \name{ionisationProducts} \alias{ionisationProducts} -\title{Ionisation Products} +\title{Ionisation products} \usage{ ionisationProducts(SMILES, adductTable = adducts()) } diff --git a/man/isotopeDistribution.Rd b/man/isotopeDistribution.Rd index 3a43201..d7882c8 100644 --- a/man/isotopeDistribution.Rd +++ b/man/isotopeDistribution.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/isotopeDistribution.R \name{isotopeDistribution} \alias{isotopeDistribution} -\title{Isotopic Distribution Calculator} +\title{Isotopic distribution calculator} \usage{ isotopeDistribution(MF, charge, limit = 9e-05, elementTable = elements()) } @@ -16,7 +16,7 @@ isotopeDistribution(MF, charge, limit = 9e-05, elementTable = elements()) \item{elementTable}{the table containing elemental information. Defaults to \code{Elements}.} } \description{ -Isotopic Distribution Calculator +Isotopic distribution calculator } \examples{ res <- isotopeDistribution('C4H5O5',charge = -1) diff --git a/man/isotopes.Rd b/man/isotopes.Rd index babf900..56e055c 100644 --- a/man/isotopes.Rd +++ b/man/isotopes.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/data.R \name{isotopes} \alias{isotopes} -\title{isotopes} +\title{Isotopic rules} \format{ A tibble containing 8 rows and 3 columns. \describe{ diff --git a/man/metaboliteDB.Rd b/man/metaboliteDB.Rd index 4f46456..d5aee2c 100644 --- a/man/metaboliteDB.Rd +++ b/man/metaboliteDB.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/metaboliteDB.R \name{metaboliteDB} \alias{metaboliteDB} -\title{metaboliteDB} +\title{Create a metabolite database} \usage{ metaboliteDB(accessions, descriptors, connection = NULL, type = "local") } diff --git a/man/mzAnnotation.Rd b/man/mzAnnotation.Rd deleted file mode 100644 index 1346ee9..0000000 --- a/man/mzAnnotation.Rd +++ /dev/null @@ -1,8 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/mzAnnotation.R -\name{mzAnnotation} -\alias{mzAnnotation} -\title{mzAnnotation} -\description{ -mzAnnotation -} diff --git a/man/ppmError.Rd b/man/ppmError.Rd index ce16863..f7544c7 100644 --- a/man/ppmError.Rd +++ b/man/ppmError.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/ppmError.R \name{ppmError} \alias{ppmError} -\title{ppmError} +\title{Calculate PPM error} \usage{ ppmError(measured, theoretical) } diff --git a/man/ppmRange.Rd b/man/ppmRange.Rd index acee6a4..182c0fc 100644 --- a/man/ppmRange.Rd +++ b/man/ppmRange.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/RcppExports.R \name{ppmRange} \alias{ppmRange} -\title{ppmRange} +\title{Calculate a PPM error range} \usage{ ppmRange(mz, ppm) } diff --git a/man/smartsSearch.Rd b/man/smartsSearch.Rd index 3e0bac4..348bfb3 100644 --- a/man/smartsSearch.Rd +++ b/man/smartsSearch.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/RcppExports.R \name{smartsSearch} \alias{smartsSearch} -\title{smartsSearch} +\title{SMARTS substructure search} \usage{ smartsSearch(smile, smart) } diff --git a/man/smileToAccurateMass.Rd b/man/smileToAccurateMass.Rd index a0d06aa..3608fe1 100644 --- a/man/smileToAccurateMass.Rd +++ b/man/smileToAccurateMass.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/RcppExports.R \name{smileToAccurateMass} \alias{smileToAccurateMass} -\title{smileToAccurateMass} +\title{Convert SMILES to accurate mass} \usage{ smileToAccurateMass(smile) } diff --git a/man/smileToMF.Rd b/man/smileToMF.Rd index 76d3bcf..7521826 100644 --- a/man/smileToMF.Rd +++ b/man/smileToMF.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/RcppExports.R \name{smileToMF} \alias{smileToMF} -\title{smileToMF} +\title{Convert SMILES to molecular formula} \usage{ smileToMF(smile) } diff --git a/man/transformMF.Rd b/man/transformMF.Rd index 68ac022..1937caf 100644 --- a/man/transformMF.Rd +++ b/man/transformMF.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/transformMF.R \name{transformMF} \alias{transformMF} -\title{transformMF} +\title{Transform a molecular formula} \usage{ transformMF( MF, diff --git a/man/transformations.Rd b/man/transformations.Rd index 3b451ff..e889bb8 100644 --- a/man/transformations.Rd +++ b/man/transformations.Rd @@ -2,7 +2,7 @@ % Please edit documentation in R/data.R \name{transformations} \alias{transformations} -\title{transformations} +\title{Transformation rules} \format{ A tibble containing 12 rows and 9 columns. \describe{ diff --git a/src/conversion.cpp b/src/conversion.cpp index 30800e8..60d3178 100644 --- a/src/conversion.cpp +++ b/src/conversion.cpp @@ -22,7 +22,7 @@ std::string cnvrt(std::string input,const char* inputType,const char* outputType return res; } -//' smileToMF +//' Convert SMILES to molecular formula //' @description convert a smile to a molecular formula //' @param smile a valid SMILE //' @examples @@ -41,7 +41,7 @@ std::string smileToMF(std::string smile){ return res; } -//' smileToAccurateMass +//' Convert SMILES to accurate mass //' @description convert a smile to an accurate mass //' @param smile a valid SMILE //' @examples diff --git a/src/descriptors.cpp b/src/descriptors.cpp index 6ff3716..1f15278 100644 --- a/src/descriptors.cpp +++ b/src/descriptors.cpp @@ -7,7 +7,7 @@ using namespace OpenBabel; #include using namespace Rcpp; -//' smartsSearch +//' SMARTS substructure search //' @description SMARTS substructure searching for SMILES. //' @param smile a valid SMILE //' @param smart a valid SMARTS symbol diff --git a/src/ppmRange.cpp b/src/ppmRange.cpp index e5b1ce7..959422d 100644 --- a/src/ppmRange.cpp +++ b/src/ppmRange.cpp @@ -1,7 +1,7 @@ #include using namespace Rcpp; -//' ppmRange +//' Calculate a PPM error range //' @description Calculate the upper and lower ppm boundaries for a given m/z //' @param mz the m/z for which to calculate the range //' @param ppm the ppm From a44cb50ee9e39466c85b548201418139bd05e8a2 Mon Sep 17 00:00:00 2001 From: jasenfinch Date: Wed, 17 Feb 2021 23:40:15 +0000 Subject: [PATCH 24/24] updated package url --- .Rbuildignore | 3 +++ .gitignore | 3 ++- DESCRIPTION | 3 ++- _pkgdown.yml | 1 + 4 files changed, 8 insertions(+), 2 deletions(-) create mode 100644 _pkgdown.yml diff --git a/.Rbuildignore b/.Rbuildignore index df8db67..36b4e8d 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -12,3 +12,6 @@ README* ^codecov\.yml$ LICENSE ^\.github$ +^_pkgdown\.yml$ +^docs$ +^pkgdown$ diff --git a/.gitignore b/.gitignore index bd2cf34..6c83575 100644 --- a/.gitignore +++ b/.gitignore @@ -5,4 +5,5 @@ Read-and-delete-me mfGen.o RcppExports.o mzAnnotation.dll -mzAnnotation.so \ No newline at end of file +mzAnnotation.so +docs diff --git a/DESCRIPTION b/DESCRIPTION index a991e21..06b066e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,7 +9,8 @@ Authors@R: Description: Tools for the putative annotation of high resolution metabolomics m/z. data. biocViews: MassSpectrometry, Metabolomics -URL: https://github.com/jasenfinch/mzAnnotation +URL: https://jasenfinch.github.io/pdi/ +BugReports: https://github.com/jasenfinch/mzAnnotation/issues Depends: R (>= 3.5) Imports: Rcpp, diff --git a/_pkgdown.yml b/_pkgdown.yml new file mode 100644 index 0000000..3e55cb6 --- /dev/null +++ b/_pkgdown.yml @@ -0,0 +1 @@ +url: https://jasenfinch.github.io/mzAnnotation/