batchPick: Batch pick raw mzXML files

In meowcat/RMassScreening: Suspect screening and time series in LC-HRMS data

Description

Peak picking using mostly enviPick. The function handles polarity switching raw files and parallel picking on multiple cores. batchPickDIA additionally handles DIA files, including polarity switching DIA files, and picks every DIA scan separately.

Usage

batchPick(files, outputDir, polarity = c("+", "-"), writeData = TRUE,
  writeList = TRUE, settings = getOption("RMassScreening")$enviPick,
  multicore = FALSE, log = "logCluster.txt")

batchPickDIA(files, outputDir, writeData = TRUE, writeList = TRUE,
  settings = getOption("RMassScreening")$enviPick, multicore = FALSE,
  log = "logCluster.txt")

comprehensiveBatchPick(...)

Arguments

files	Array of paths to the raw files.
outputDir	Folder to write picked file results to.
polarity	For batchPick, +or -. Selects the polarity to pick. On one hand, this is needed to handle polarity switching files correctly; on the other hand, it also determines the file names to use downstream.
writeData	If TRUE, the picked file object (the MSlist from enviPick) is saved to disk
writeList	If TRUE, the CSV picked peak table is saved to disk
settings	Settings to use for enviPick. Read the settings file template for descriptions, or the enviPick documentation accordingly. By default uses the settings as loaded.
multicore	FALSE for single core processing, or an integer number for the number of cores to use.
log	Logfile output for multicore processing (irrelevant for single core).

Details

Warning: batchPick doesn't actually use the settings at all! only batchPickDIA does.

batchPick picks either positive or negative mode data as specified. For a raw file RAWFILE.mzXML, the picked files (writeData output) have names RAWFILE.mzXML.MSlist.pos.RData for positive mode, or .neg.RData for negative mode respectively. For writeList, the files are .csv instead.

For batchPickDIA, the file names follow the pattern RAWFILE.mzXML.MSlist.LEVEL-POLARITY-CENTER-WIDTH.RData. For the MS1 scans, this is e.g. 1-pos-- because there is no isolation center or isolation width. For the MS2 scans, a positive scan with center 400 and isolation width 200 would have 2-pos-400-200 in the name.

For legacy reasons, batchPick produces the objects MSlist.pos and MSlist.neg respectively, whereas batchPickDIA only makes MSlist regardless of polarity.

batchPick will soon be deprecated (or rather batchPickDIA will take over the name.)

If multicore is used, the processing messages ("output") are piped to the logfile. For single core, the output is displayed on screen.

Value

For batchPickDIA, returns a character vector of all scan types picked (the filename patterns for use in fillProfiles etc.).

Functions

• batchPickDIA:

• comprehensiveBatchPick:

Note

batchPickDIA is the new name for comprehensiveBatchPick, which should not be used anymore.

Author(s)

stravsmi

meowcat/RMassScreening documentation built on Jan. 9, 2020, 10:49 p.m.