xsAnnotate: xsAnnotate constructor for an provided xcmsSet object

In sneumann/CAMERA: Collection of annotation related methods for mass spectrometry data

xsAnnotate constructor for an provided xcmsSet object

Description

This function deals with the construction of an xsAnnotate object. It extracts the peaktable from a provided xcmsSet, which is used for all further analysis. The xcmsSet can be a single sample or multiple sample experiment. Since some functions needs the raw data a selection algorithm must be choosen in the case of a multiple sample. CAMERA includes two different strategies: A defined selection of samples (sample = indices of samples) or the default automatic solution (sample = NA). The automatic solution chooses the best sample for a specifc groups called pseudospectrum, see groupFWHM and groupCorr. It returns a xsAnnotate object, see xsAnnotate-class.

Usage

  xsAnnotate(xs = NULL, sample=NA, nSlaves = 1, polarity = NULL)

Arguments

xs	a xcmsSet object
sample	Indices of the group xcmsSet sample, that are used for the EIC correlation step. For automatic selection don't set a value. For use all samples simply define sample = c(1:n), with n = number of samples.
nSlaves	For parallel mode set nSlaves higher than 1, but not higher than the number of cpu cores.
polarity	Set polarity mode: "positive" or "negative"

Value

A xsAnnotate object.

Author(s)

Carsten Kuhl, [e-mail]

See Also

xsAnnotate-class

Examples

 library(faahKO)
 xs <- group(faahko)
 xsa <- xsAnnotate(xs, sample=c(1:12))

 #With automatic selection
 xsa.autoselect <- xsAnnotate(xs)

sneumann/CAMERA documentation built on April 5, 2024, 2:33 a.m.