MSnbase: isCentroidedFromFile – R documentation

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isCentroidedFromFile

Get mode from mzML data file

Description

The function extracts the mode (profile or centroided) from the raw mass spectrometry file by parsing the mzML file directly. If the object x stems from any other type of file, NAs are returned.

Usage

isCentroidedFromFile(x)

Arguments

`x`	An object of class OnDiskMSnExp.

Details

This function is much faster than isCentroided(), which estimates mode from the data, but is limited to data stemming from mzML files which are still available in their original location (and accessed with fileNames(x)).

Value

A named logical vector of the same length as x.

Author(s)

Laurent Gatto

Examples

library("msdata")
f <- proteomics(full.names = TRUE,
                pattern = "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML.gz")
x <- readMSData(f, mode = "onDisk")
table(isCentroidedFromFile(x), msLevel(x))

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