R/FDR_calculator_nokb.R

In akivab2/Analyze4CPackage: Analysis Of 4C Data

#' @export

FDR_calculator_nokb <- function(filename_raw,small.RE,big.RE,step.RE,small.CO,big.CO,step.CO,vp.chrom,vp.pos,erase,cyc)
{
	sz <- (floor((big.RE-small.RE)/step.RE)+1)*(round((big.CO-small.CO)/step.CO)+1); #getting the number of all the elements that will be checked
	ind_count <- 0; #this counts the index for each column in the data frame
	window_RE <- rep(0,sz);
	CO <- rep(0,sz);
	fdr.avg.trans <- rep(0,sz);
	fdrs <- c()
	ln <- length(unique(filename_raw[,1])); #getting the number of chromosomes
	counter <- 0
	for(i in seq(small.RE,big.RE,by=step.RE))
	{
		ps <- pScore_nokb(filename_raw,vp.chrom,vp.pos,erase,i); #calculating p score with current window size
		for(j in seq(small.CO,big.CO,by=step.CO))
		{
			counter <- counter + 1
			cat("\ncalculating",cyc,"cycles for round",counter,"out of",sz,"\n\n")
			fdr.temp <- FDR_nokb_noPrint(ps,filename_raw,vp.chrom,vp.pos,erase,i/2,cyc,j); #calculating FDR with current cutoff percent
			fdr.sum <- sum(fdr.temp)-fdr.temp[vp.chrom]; #getting the sum of fdr from trans
			fdr.avg <- fdr.sum/(ln-1); #getting the average of fdr from trans

			#creating the columns for the data frame
			ind_count <- ind_count + 1;
			window_RE[ind_count] <- i;
			CO[ind_count] <- j;	
			fdr.avg.trans[ind_count] <- fdr.avg;
			fdrs <- rbind(fdrs,fdr.temp)
		}
	}
	#getting the chromosome names/numbers and adding them as the column names in 'fdrs'
	chrs <- unique(filename_raw[,1])
	chr_names <- rep(0,ln)
	for(t in 1:ln)
	{
		chr_names[t] <- paste("chr",chrs[t],sep="")
	}
	fdrs <- t(as.data.frame(fdrs))
	rownames(fdrs) <- chr_names
	fdrs <- t(fdrs)
	rownames(fdrs) <- seq(1:nrow(fdrs))
		
	all <- data.frame(window_RE,CO,fdrs,fdr.avg.trans); #creating the data frame
	print(all)
	return(all);
}