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Read an 'mzTab' file

Source: R/readWriteMzTab.R
readMzTabData_v0.9.Rd

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.

Usage

readMzTabData_v0.9(file, what = c("PRT", "PEP"), verbose = isMSnbaseVerbose())

Arguments

file

A character with the mzTab file to be read in.

what

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.

verbose

Produce verbose output.

Value

An instance of class MSnSet.

See also

writeMzTabData to save an "MSnSet" as an mzTab file.

Author

Laurent Gatto

Examples

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: Tue Oct 15 15:27:19 2024 
#>  MSnbase version: 2.31.2 

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: Tue Oct 15 15:27:19 2024 
#>  MSnbase version: 2.31.2