Description Usage Arguments Details Value Functions Note Author(s)
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.
1 2 3 4 5 6 7 8 9 | 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(...)
|
files |
Array of paths to the raw files. |
outputDir |
Folder to write picked file results to. |
polarity |
For |
writeData |
If |
writeList |
If |
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 |
|
log |
Logfile output for multicore processing (irrelevant for single core). |
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.
For batchPickDIA
, returns a character vector of all scan types picked (the filename patterns for use in fillProfiles
etc.).
batchPickDIA
:
comprehensiveBatchPick
:
batchPickDIA
is the new name for comprehensiveBatchPick
, which should not be used anymore.
stravsmi
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