getSumreplicateschild <-
function(curdata,alignment.tool,numreplicates,rep.max.missing.thresh,method="mean",missing.val)
{
#curdata<-t(curdata)
#write.table(curdata,file="test.txt",sep="\t",row.names=FALSE)
numfeats=dim(curdata)[1]
numsamp=dim(curdata)[2]
# if(FALSE){
resvec_1<-lapply(1:numfeats,function(r)
{
newrow={}
finalmat={}
#for(samp in seq(1,(numsamp),numreplicates))
{
# i=samp
#j=i+numreplicates-1
curdata_int=curdata[r,]
#if(is.na(missing.val)==FALSE){
# check_zeros=which(curdata_int==missing.val)
# }else{
check_zeros=which(is.na(curdata_int)==TRUE)
# }
na_thresh=round(rep.max.missing.thresh*numreplicates)
if(length(check_zeros)>na_thresh)
{
meanval<-missing.val
}
else
{
#temporarily replace the missing intensities, set to 0 in apLCMS,
#with mean intensity value of the corresponding replicates (with non-zero values)
#curdata_int[check_zeros]=mean(t(curdata_int[-c(check_zeros)]))
if(length(check_zeros)>0)
{
if(method=="mean"){
meanval<-mean(t(curdata_int[-check_zeros]),na.rm=TRUE)
}else{
meanval<-median(t(curdata_int[-check_zeros]),na.rm=TRUE)
}
}
else
{
if(method=="mean"){
meanval<-mean(t(curdata_int),na.rm=TRUE)
}else{
meanval<-median(t(curdata_int),na.rm=TRUE)
}
}
}
newrow<-cbind(newrow,meanval)
}
finalmat<-rbind(finalmat, newrow)
return(finalmat)
})
#colnames(final_set)<-colnames_data
#rownames(final_set)=NULL
return(resvec_1)
}
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