MSnbase: mzRident2dfr – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

mzRident2dfr

Coerce identification data to a data.frame

Description

A function to convert the identification data contained in an mzRident object to a data.frame. Each row represents a scan, which can however be repeated several times if the PSM matches multiple proteins and/or contains two or more modifications. To reduce the data.frame so that rows/scans are unique and use semicolon-separated values to combine information pertaining a scan, use reduce.

Arguments

from

An object of class mzRident defined in the mzR package.

Details

See also the Tandem MS identification data section in the MSnbase-demo vignette.

Value

A data.frame

Author(s)

Laurent Gatto

Examples

## find path to a mzIdentML file
identFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
                 full.name = TRUE, pattern = "dummyiTRAQ.mzid")
library("mzR")
x <- openIDfile(identFile)
x
as(x, "data.frame")

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