filter.by.missing.values <-
function(data_m,missing.val=0,all.missing.thresh=0.5){
##################################################################################
metab_zeros={}
data_clean<-{}
clean_metabs<-{}
if(is.na(all.missing.thresh)==FALSE)
{
total_sigs<-apply(data_m,1,function(x){
#if missing.val=0 or a non NA value
if(is.na(missing.val)==FALSE){return(length(which(x>missing.val)))
}else{
#if missing.val=NA
return(length(which(is.na(x)==FALSE)))
}})
total_sig_thresh<-dim(data_m)[2]*all.missing.thresh
total_good_metabs<-which(total_sigs>total_sig_thresh)
}else{
total_good_metabs<-seq(1,nrow(data_m))
}
#remove bad features based on all missing values criteria
if(length(total_good_metabs)>0){
data_m<-data_m[total_good_metabs,]
print(paste("Dimension of data matrix after using overall ",100*all.missing.thresh, "% signal criteria for filtering:"),sep="")
print(dim(data_m))
}else{
#stop(paste("None of the have signal in ",all.missing.thresh*100, "% of samples",sep=""))
data_m<-{}
}
return(data_m)
}
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