Package 'IDSL.MXP'

getNetCDF

Description

This function returns a list of two data objects needed for the mass spectrometry data processing.

Usage

getNetCDF(MSfile)

Arguments

MSfile

name of the mass spectrometry file with .cdf extension

Value

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'.

spectraList

a list of matrices of m/z and intensity values for each chromatogram scan

Note

‘retentionTime' column in the 'scanTable’ object is presented in minute.

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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")

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getSpectra

Description

This function creates a spectraList for the chromatogram scans of the mass spectrometry data.

Usage

getSpectra(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 list of matrices of m/z and intensity values for each chromatogram scan

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"))
spectraList <- getSpectra(xmlData, msFormat = "mzML")

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MXP Locate regex

Description

Locate indices of the pattern in the string

Usage

MXP_locate_regex(string, pattern, ignore.case = FALSE, perl = FALSE, fixed = FALSE,
useBytes = FALSE)

Arguments

string	a string as character
pattern	a pattern to screen
ignore.case	ignore.case
perl	perl
fixed	fixed
useBytes	useBytes

Details

This function returns 'NULL' when no matches are detected for the pattern.

Value

A 2-column matrix of location indices. The first and second columns represent start and end positions, respectively.

Examples

pattern <- "Cl"
string <- "NaCl.5HCl"
Location_Cl <- MXP_locate_regex(string, pattern)

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Peak to List (The main function)

Description

This function returns a list of two data objects required for the mass spectrometry data processing.

Usage

peak2list(path, MSfileName = "")

Arguments

path	address of the mass spectrometry file
MSfileName	name of the mass spectrometry file with .mzML or .mzXML extensions

Value

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

Note

‘retentionTime' column in the 'scanTable’ object is presented in minute.

See Also

https://colab.research.google.com/drive/1gXwwuI1zzDHykKfodLSQQt5rwTuFEMpD

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)
p2l <- peak2list(path = temp_wd, MSfileName = "003.mzML")

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