xsAnnotate: xsAnnotate constructor for an provided xcmsSet object

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

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)

CAMERA documentation built on Nov. 8, 2020, 4:59 p.m.