comparison corr.R @ 9:ecad2cd5038f

debug message was making truble

8:44920cae2f4d

    suppressWarnings(Reduce(union, coverages)) #supress because missing chromosomes spit warinings
}

## adds mappable regions as 0 coverage to track 
covWith0 <- function(cov, mappable){
    print(paste("cov:",cov))
	c0 <- setdiff(mappable, cov)
    cus <- if(length(c0) > 0){
	  elementMetadata(c0)$score <- 0
      sort(c(c0, cov))
	}else{

getCoverages <- function(infiles, formats){
   apply(data.frame(file=infiles,format=formats),1, function(row){ getCoverage(row['file'], row['format']) })
}

getMappable <- function(coverages, mappable){
    print(paste("creating mappability", mappable))
	if(is.na(mappable)){
	    createMappable(coverages)
    }else{
        import(mappable, format="bed", asRangedData = FALSE)
    }

9:ecad2cd5038f

    suppressWarnings(Reduce(union, coverages)) #supress because missing chromosomes spit warinings
}

## adds mappable regions as 0 coverage to track 
covWith0 <- function(cov, mappable){
    print(paste("cov:", summary(cov)))
	c0 <- setdiff(mappable, cov)
    cus <- if(length(c0) > 0){
	  elementMetadata(c0)$score <- 0
      sort(c(c0, cov))
	}else{

getCoverages <- function(infiles, formats){
   apply(data.frame(file=infiles,format=formats),1, function(row){ getCoverage(row['file'], row['format']) })
}

getMappable <- function(coverages, mappable){
    print(paste("creating mappability", length(coverages), mappable))
	if(is.na(mappable)){
	    createMappable(coverages)
    }else{
        import(mappable, format="bed", asRangedData = FALSE)
    }