nucleR (version 2.4.0)

coverage.rpm: Coverage calculation and normalization to reads per million (rpm)

Description

Calculates the coverage values from a RangedData object (or anything with a defined coverage function associated) and returns the coverage normalized to reads per million, allowing the comparison of experiments with a different absolut number of reads.

Usage

coverage.rpm(data, scale=1e6, ...)

Arguments

data

RangedData (or compatible) with the reads information

scale

By default, a million (1e6), but you could change this value for abnormal high or low amount of reads

...

Additional arguments to be passed to coverage function

Value

RleList object with the coverage objects

See Also

processReads, coverage

Examples

	
	#Load the example dataset and get the coverage
	data(nucleosome_htseq)
	cov = coverage.rpm(nucleosome_htseq)

	print(cov)

	#Plot it
	plot(as.vector(cov[["chr1"]]), type="l", ylab="coverage", xlab="position")