PanNETsubtypesmicRNAVal <-function(Indata,IndSAMdata)
{
# Selecting non-redudant genes
res1<-screenExpr(Indata,0)
cat("Data after screenExpr has", ncol(res1)-1, "samples", "\n", append = T)
sdv<-paste("_sd0.txt",sep="")
InputFileName_sd<-paste("241210-Weidenmann-49-samples-data-genesonly_1_sd0_removed_non_PNET_few_Mets",sdv,sep="")
# Creating storage for results and setting the working directory
dir.create("PanNETassignerResults", showWarnings = FALSE)
dir.create("PanNETassignerResults/micRNAVal", showWarnings = FALSE)
dir<-getwd()
setwd(paste0(dir,"/PanNETassignerResults/micRNAVal"))
# Selecting SAM genes sam<-IndSAMdata
sam<-IndSAMdata
sam_mat<-match(sam[,1],res1[,1])
sam_w<-which(!is.na(sam_mat))
data_sam<-res1[sam_mat[sam_w],]
InputFileName_sam<-paste((strsplit(InputFileName_sd,".txt")[1]),"_SAM.txt",sep="")
write.table(data_sam,InputFileName_sam, row.names=FALSE,sep="\t",quote=FALSE)
dataUnique<-apply(data.matrix(data_sam[,2:dim(res1)[2]]),2,as.numeric)
rownames(dataUnique)<-data_sam[,1]
# Median centering data
rowMed <- apply(dataUnique,1,median, na.rm=TRUE);
dataUnique<-dataUnique-rowMed
dataUnique_1<-cbind(rownames(dataUnique),dataUnique)
InputFileName_sam_med<-paste((strsplit(InputFileName_sam,".txt")[1]),"_data_cdt.txt",sep="")
write.table(dataUnique_1,InputFileName_sam_med, row.names=FALSE,sep="\t",quote=FALSE)
# NMF analysis
cat("Performing NMF analysis...")
nmfconsensus(input.ds=InputFileName_sam_med,k.init=2,k.final=4,num.clusterings=20,maxniter=500, error.function="euclidean",data=dataUnique)
k=1:5
# Ordering samples by NMF consensus k=3 cluster
con<-read.delim("consensus.k.3.gct", stringsAsFactors=FALSE)
m<-match(con[,1],colnames(dataUnique_1))
#m
InputFileName_sam_med_NMF<-paste((strsplit(InputFileName_sam_med,".txt")[1]),"_NMF_ordered_3.txt",sep="")
data_2<-cbind(dataUnique_1[,1],dataUnique_1[,m])
write.table(data_2,InputFileName_sam_med_NMF, row.names=FALSE,sep="\t",quote=FALSE)
setwd(dir)
}
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