MSnbase: extractSpectraData – R documentation

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

extractSpectraData

Extract data from MSnbase objects for use in Spectra

Description

extractSpectraData extracts the spectra data (m/z and intensity values including metadata) from MSnExp, OnDiskMSnExp, Spectrum1, Spectrum2 objects (or list of such objects) and returns these as a DataFrame that can be used to create a Spectra::Spectra object.This function enables thus to convert data from the old MSnbase package to the newer Spectra package.

Usage

extractSpectraData(x)

Arguments

`x`	a `list` of Spectrum objects or an object extending MSnExp or a MSpectra object.

Value

DataFrame() with the full spectrum data that can be passed to the Spectra::Spectra() function to create a Spectra object.

Author(s)

Johannes Rainer

Examples

## Read an mzML file with MSnbase
fl <- system.file("TripleTOF-SWATH", "PestMix1_SWATH.mzML",
    package = "msdata")
data <- filterRt(readMSData(fl, mode = "onDisk"), rt = c(1, 6))

## Extract the data as a DataFrame
res <- extractSpectraData(data)
res

## This can be used as an input for the Spectra constructor of the
## Spectra package:
## sps <- Spectra::Spectra(res)
## sps

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