diff --git a/docs/index.html b/docs/index.html index 424b03f..5dad3ba 100644 --- a/docs/index.html +++ b/docs/index.html @@ -288,7 +288,7 @@

Setup
+
source("https://raw.githubusercontent.com/rformassspectrometry/book/main/install_docs_deps.R")

Acknowledgments
diff --git a/docs/sec-id.html b/docs/sec-id.html index 18a73b9..46b5bfd 100644 --- a/docs/sec-id.html +++ b/docs/sec-id.html @@ -1125,7 +1125,7 @@

## [local] QEP2LC6_HeLa_50ng_251120_03-calib.mzID.gz ## [local] QEP2LC6_HeLa_50ng_251120_03-calib.mzML ## [remote] QEP2LC6_HeLa_50ng_251120_03.raw -## [remote] QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz +## [local] QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz ## ... 
(mzids <- pxget(PXD022816, grep("mzID", pxfiles(PXD022816))[1:3]))
## Project PXD022816 files (32):
@@ -1138,7 +1138,7 @@ 

 ##  [local]  QEP2LC6_HeLa_50ng_251120_03-calib.mzID.gz
 ##  [local]  QEP2LC6_HeLa_50ng_251120_03-calib.mzML
 ##  [remote] QEP2LC6_HeLa_50ng_251120_03.raw
-##  [remote] QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz
+##  [local]  QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz
 ##  ...
## Warning in rep(as.integer(len), length = length(str)): partial argument match
 ## of 'length' to 'length.out'
@@ -1163,7 +1163,7 @@

## [local] QEP2LC6_HeLa_50ng_251120_03-calib.mzID.gz ## [local] QEP2LC6_HeLa_50ng_251120_03-calib.mzML ## [remote] QEP2LC6_HeLa_50ng_251120_03.raw -## [remote] QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz +## [local] QEP2LC6_HeLa_50ng_251120_04-calib.mzID.gz ## ... 
## Warning in rep(as.integer(len), length = length(str)): partial argument match
 ## of 'length' to 'length.out'
@@ -1388,7 +1388,7 @@

## 77 2 3563.78 26314 ## ... 65 more variables/columns. ## Processing: -## Switch backend from MsBackendMzR to MsBackendDataFrame [Mon Mar 18 09:11:06 2024] +## Switch backend from MsBackendMzR to MsBackendDataFrame [Mon Mar 18 14:05:02 2024] 
cmat <- compareSpectra(sp_O43175)
 rownames(cmat) <-
     colnames(cmat) <- strtrim(sp_O43175$sequence, 3)
diff --git a/docs/sec-raw.html b/docs/sec-raw.html
index 74d91e7..700ff94 100644
--- a/docs/sec-raw.html
+++ b/docs/sec-raw.html
@@ -491,7 +491,7 @@ 

 ## 1862         1   259.752       931
 ##  ... 33 more variables/columns.
 ## Processing:
-##  Switch backend from MsBackendMzR to MsBackendMemory [Mon Mar 18 09:10:18 2024]
+## Switch backend from MsBackendMzR to MsBackendMemory [Mon Mar 18 14:04:22 2024]
  • MsBackendHdf5Peaks: similar to MsBackendMzR this backend reads peak data @@ -523,7 +523,7 @@

    ## 20171016_POOL_POS_1_105-134.h5 ## 20171016_POOL_POS_3_105-134.h5 ## Processing: -## Switch backend from MsBackendMzR to MsBackendHdf5Peaks [Mon Mar 18 09:10:24 2024] +## Switch backend from MsBackendMzR to MsBackendHdf5Peaks [Mon Mar 18 14:04:29 2024] 
    table(sp_hdf5$dataOrigin)
    ## 
 ## /home/lgatto/disk/R/x86_64-pc-linux-gnu-library/4.3/msdata/sciex/20171016_POOL_POS_1_105-134.mzML 
@@ -532,9 +532,9 @@ 
    
 ##                                                                                               931
    table(sp_hdf5$dataStorage)
    ## 
-## /tmp/RtmpKu4Alm/20171016_POOL_POS_1_105-134.h5 
+## /tmp/RtmpJ3ldDf/20171016_POOL_POS_1_105-134.h5 
 ##                                            931 
-## /tmp/RtmpKu4Alm/20171016_POOL_POS_3_105-134.h5 
+## /tmp/RtmpJ3ldDf/20171016_POOL_POS_3_105-134.h5 
 ##                                            931

    All of the above mentioned backends support changing all of their their spectra variables, except the MsBackendMzR that does not support changing m/z or @@ -658,7 +658,7 @@

    ## file(s): ## 678521a4fbe2_TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzML ## Processing: -## Filter: select parent/children scans for 2807 [Mon Mar 18 09:10:25 2024] +## Filter: select parent/children scans for 2807 [Mon Mar 18 14:04:29 2024]

    @@ -972,8 +972,8 @@

    ## file(s): ## 20171016_POOL_POS_3_105-134.mzML ## Processing: -## Filter: select data origin(s) /home/lgatto/disk/R/x86_64-pc-linux-gnu-library/4.3/msdata/sciex/20171016_POOL_POS_3_105-134.mzML [Mon Mar 18 09:10:26 2024] -## Filter: select retention time [175..189] on MS level(s) 1 [Mon Mar 18 09:10:26 2024] +## Filter: select data origin(s) /home/lgatto/disk/R/x86_64-pc-linux-gnu-library/4.3/msdata/sciex/20171016_POOL_POS_3_105-134.mzML [Mon Mar 18 14:04:31 2024] +## Filter: select retention time [175..189] on MS level(s) 1 [Mon Mar 18 14:04:31 2024]

    @@ -1059,7 +1059,7 @@

    ## 20171016_POOL_POS_3_105-134.mzML ## Lazy evaluation queue: 1 processing step(s) ## Processing: -## Remove peaks with intensities outside [10, Inf] in spectra of MS level(s) 1. [Mon Mar 18 09:10:26 2024] +## Remove peaks with intensities outside [10, Inf] in spectra of MS level(s) 1. [Mon Mar 18 14:04:31 2024] 
    min(intensity(sp_sciex[1]))
    ## [1] 412
    sp_sciex@processingQueue