| getScanTable {IDSL.MXP} | R Documentation |
getScanTable
Description
This function creates a scanTable from chromatogram scans of the mass spectrometry data.
Usage
getScanTable(xmlData, msFormat)
Arguments
xmlData |
A structured data of the mass spectrometry data created by the 'read_xml' function. |
msFormat |
format extension of the mass spectrometry file c("mzML", "mzXML") |
Value
a dataframe of different scan properties including 'seqNum', 'msLevel', 'polarity', 'peaksCount', 'totIonCurrent', 'retentionTime', 'basePeakMZ', 'basePeakIntensity', 'collisionEnergy', 'lowMZ', 'highMZ', 'precursorScanNum', 'precursorMZ', 'precursorCharge', 'precursorIntensity', 'injectionTime', 'filterString', 'scanType', 'centroided', 'isolationWindowTargetMZ', 'isolationWindowLowerOffset', 'isolationWindowUpperOffset', 'scanWindowLowerLimit', and 'scanWindowUpperLimit'. 'scanType' is only provided for the mzXML data format.
Note
'retentionTime' column is presented in minute.
Examples
temp_wd <- tempdir()
temp_wd_zip <- paste0(temp_wd,"/idsl_ipa_test_files.zip")
download.file(paste0("https://github.com/idslme/IDSL.IPA/blob/main/",
"IPA_educational_files/idsl_ipa_test_files.zip?raw=true"),
destfile = temp_wd_zip, mode = "wb")
unzip(temp_wd_zip, exdir = temp_wd)
xmlData <- xml2::read_xml(paste0(path = temp_wd, "/", MSfile = "003.mzML"))
scanTable <- getScanTable(xmlData, msFormat = "mzML")