readMzTabData: Read an 'mzTab' file

Description Usage Arguments Value Author(s) See Also Examples

View source: R/readWriteMzTab.R

Description

This function can be used to create an "MSnSet" by reading and parsing an mzTab file. The metadata section is always used to populate the MSnSet's experimentData()@other$mzTab slot.

Usage

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readMzTabData(
  file,
  what = c("PRT", "PEP", "PSM"),
  version = c("1.0", "0.9"),
  verbose = isMSnbaseVerbose()
)

Arguments

file

A character with the mzTab file to be read in.

what

One of "PRT", "PEP" or "PSM", defining which of protein, peptide PSMs section should be returned as an MSnSet.

version

A character defining the format specification version of the mzTab file. Default is "1.0". Version "0.9" is available of backwards compatibility. See readMzTabData_v0.9 for details.

verbose

Produce verbose output.

Value

An instance of class MSnSet.

Author(s)

Laurent Gatto

See Also

See MzTab and MSnSetList for details about the inners of readMzTabData.

Examples

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testfile <- "https://raw.githubusercontent.com/HUPO-PSI/mzTab/master/examples/1_0-Proteomics-Release/PRIDE_Exp_Complete_Ac_16649.xml-mztab.txt"

prot <- readMzTabData(testfile, "PRT")

prot

head(fData(prot))

head(exprs(prot))

psms <- readMzTabData(testfile, "PSM")

psms

head(fData(psms))

MSnbase documentation built on Jan. 23, 2021, 2 a.m.