MSnbase: readMzTabData – R documentation

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readMzTabData

Read an 'mzTab' file

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

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

Examples

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

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release