peak2list {IDSL.MXP} | R Documentation |
This function returns a list of two data objects required for the mass spectrometry data processing.
peak2list(path, MSfileName = "")
path |
address of the mass spectrometry file |
MSfileName |
name of the mass spectrometry file with .mzML or .mzXML extensions |
scanTable |
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. |
spectraList |
a list of matrices of m/z and intensity values for each chromatogram scan |
‘retentionTime' column in the 'scanTable’ object is presented in minute.
https://colab.research.google.com/drive/1gXwwuI1zzDHykKfodLSQQt5rwTuFEMpD
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)
p2l <- peak2list(path = temp_wd, MSfileName = "003.mzML")