| Type: | Package |
| Title: | Parser for mzML, mzXML, and netCDF Files (Mass Spectrometry Data) |
| Version: | 2.0 |
| Depends: | R (≥ 4.0) |
| Imports: | xml2, base64enc |
| Suggests: | RNetCDF |
| Author: | Sadjad Fakouri-Baygi
 [aut],
Dinesh Barupal
[cre, aut] |
| Maintainer: | Dinesh Barupal <dinesh.barupal@mssm.edu> |
| Description: | A tiny parser to extract mass spectra data and metadata table of mass spectrometry acquisition properties from mzML, mzXML and netCDF files introduced in <doi:10.1021/acs.jproteome.2c00120>. |
| License: | MIT + file LICENSE |
| URL: | https://github.com/idslme/idsl.mxp https://colab.research.google.com/drive/1gXwwuI1zzDHykKfodLSQQt5rwTuFEMpD |
| BugReports: | https://github.com/idslme/idsl.mxp/issues |
| Encoding: | UTF-8 |
| Archs: | i386, x64 |
| NeedsCompilation: | no |
| Packaged: | 2023-03-23 16:38:45 UTC; sfbaygi |
| Repository: | CRAN |
| Date/Publication: | 2023-03-24 10:00:16 UTC |
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)
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.
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")
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")
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")