MSnbase: readMzTabData_v0.9 – R documentation

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readMzTabData_v0.9

Read an 'mzTab' file

Description

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.

Author(s)

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")

prot

pep <- readMzTabData_v0.9(testfile, "PEP")

pep

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