xsAnnotate: 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.
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.