G'day,
When calling groupCorr with the xraw argument set I see the following error message:
> groupCorr(object=yanGI, calcIso=TRUE, xraw=xcmsRaw(file))
Start grouping after correlation.
Error in peaks(xa@xcmsSet) :
error in evaluating the argument 'object' in selecting a method for function 'peaks': Error: object 'xa' not found
Looking at the source code in fct_groupCorr.R it appears the xa has not been assigned a value.
# Check LC information and calcCorr was selected
if(calcCiS && object@xcmsSet@peaks[1,"rt"] != -1){
if(!is.null(xraw)) {
#Use provided xcmsRaw
maxscans <- length(xraw@scantime)
scantimes<-list();
scantimes[[1]] <- xraw@scantime
pdata <- peaks(xa@xcmsSet)
EIC <- CAMERA:::getEICs(xraw,pdata,maxscans)
Is this a bug?
Regards,
Chris.