Merge pull request #24 from jasenfinch/devel

v1.7.3

.Rbuildignore

@@ -12,3 +12,6 @@ README*
 ^codecov\.yml$
 LICENSE
 ^\.github$
+^_pkgdown\.yml$
+^docs$
+^pkgdown$

.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: |
+          download.file('https://github.com/girke-lab/ChemmineOB/releases/download/3.0.0/openbabel3-build.zip','D:/a/openbabel3-build.zip')
+          untar('D:/a/openbabel3-build.zip',exdir = 'D:/a/openbabel3-build')
+        shell: Rscript {0}
+
       - name: Install Linux system dependencies
         if: runner.os == 'Linux'
         run: |
@@ -77,6 +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}
 

.gitignore

@@ -5,4 +5,5 @@ Read-and-delete-me
 mfGen.o
 RcppExports.o
 mzAnnotation.dll
-mzAnnotation.so
+mzAnnotation.so
+docs

DESCRIPTION

@@ -1,14 +1,16 @@
 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",
            role = c("aut", "cre"),
            email = "[email protected]")
 Description: Tools for the putative annotation of high resolution metabolomics m/z.
     data.
-URL: https://github.com/jasenfinch/mzAnnotation
+biocViews: MassSpectrometry, Metabolomics
+URL: https://jasenfinch.github.io/pdi/
+BugReports: https://github.com/jasenfinch/mzAnnotation/issues
 Depends: R (>= 3.5)
 Imports:
     Rcpp,
@@ -26,7 +28,8 @@ Encoding: UTF-8
 RoxygenNote: 7.1.1
 LazyData: true
 Suggests: testthat,
-    covr
+    covr,
+    zlibbioc
 LinkingTo: Rcpp
 Collate: allGenerics.R
     allClasses.R

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/.

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.

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 

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.

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',

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{

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

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}

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

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

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

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{

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

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

R/generateMF.R

@@ -1,4 +1,4 @@
-#' generateMF
+#' Molecular formula generation
 #' @description Molecular formula generation
 #' @param mass accurate mass
 #' @param ppm ppm tolerance

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

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()

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

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.

R/mzAnnotation.R

@@ -1,5 +1,3 @@
-#' mzAnnotation
-#' @name mzAnnotation
 #' @useDynLib mzAnnotation
 #' @importFrom Rcpp evalCpp
 

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

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

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')
 ```
@@ -29,13 +30,15 @@ library(mzAnnotation)
 ```
 
 * Adduct, isotope and biotransfromation relationship prediction
+
 ```{r}
 res <- relationshipCalculator(c(132.03023,168.00691))
 
 res
 ```
 
 * Molecular formula generation
+
 ```{r}
 res <- generateMF(342.11621,
                   element_max = c(C = 12,H = 22,N = 0,
@@ -44,12 +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,

README.md

@@ -21,9 +21,7 @@ devtools::install_github('jasenfinch/mzAnnotation')
 
 Available tools include:
 
-  - Adduct, isotope and biotransfromation relationship prediction
-
-<!-- end list -->
+-   Adduct, isotope and biotransfromation relationship prediction
 
 ``` r
 res <- relationshipCalculator(c(132.03023,168.00691))
@@ -36,9 +34,7 @@ res
 #> # … with 2 more variables: Transformation2 <lgl>, Error <dbl>
 ```
 
-  - Molecular formula generation
-
-<!-- end list -->
+-   Molecular formula generation
 
 ``` r
 res <- generateMF(342.11621,
@@ -51,9 +47,7 @@ res
 #> 1 C12H22O11  342.           0
 ```
 
-  - Isotope distribution calculation
-
-<!-- end list -->
+-   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
-
-<!-- end list -->
+-   Putative ionisation product searches
 
 ``` r
 db <- metaboliteDB(aminoAcids,descriptors(aminoAcids$SMILES))

_pkgdown.yml

@@ -0,0 +1 @@
+url: https://jasenfinch.github.io/mzAnnotation/