This function can be used to create a "MSnSet"
by reading and parsing an mzTab
file. The metadata section
is always used to populate the MSnSet
's experimentData
slot.
readMzTabData_v0.9(file, what = c("PRT", "PEP"), verbose = isMSnbaseVerbose())
A character
with the mzTab
file to be
read in.
One of "PRT"
or "PEP"
, defining which of
protein of peptide section should be parse. The metadata
section, when available, is always used to populate the
experimentData
slot.
Produce verbose output.
An instance of class MSnSet
.
writeMzTabData
to save an
"MSnSet"
as an mzTab
file.
testfile <- "https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/legacy/jmztab-1.0/examples/mztab_itraq_example.txt"
prot <- readMzTabData_v0.9(testfile, "PRT")
#> Warning: Version 0.9 is deprecated. Please see '?readMzTabData' and '?MzTab' for details.
prot
#> MSnSet (storageMode: lockedEnvironment)
#> assayData: 2 features, 4 samples
#> element names: exprs
#> protocolData: none
#> phenoData
#> sampleNames: sub[1] sub[2] sub[3] sub[4]
#> varLabels: abundance
#> varMetadata: labelDescription
#> featureData
#> featureNames: 1 2
#> fvarLabels: accession unit_id ... protein_abundance_std_error_sub[4]
#> (26 total)
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation:
#> - - - Processing information - - -
#> mzTab read: Thu Mar 14 06:11:43 2024
#> MSnbase version: 2.29.4
pep <- readMzTabData_v0.9(testfile, "PEP")
#> Warning: Version 0.9 is deprecated. Please see '?readMzTabData' and '?MzTab' for details.
pep
#> MSnSet (storageMode: lockedEnvironment)
#> assayData: 6 features, 4 samples
#> element names: exprs
#> protocolData: none
#> phenoData
#> sampleNames: sub[1] sub[2] sub[3] sub[4]
#> varLabels: abundance
#> varMetadata: labelDescription
#> featureData
#> featureNames: 1 2 ... 6 (6 total)
#> fvarLabels: sequence accession ... peptide_abundance_std_error_sub[4]
#> (23 total)
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation:
#> - - - Processing information - - -
#> mzTab read: Thu Mar 14 06:11:43 2024
#> MSnbase version: 2.29.4