count.coverage.of.noodles: count.coverage.of.noodles

In favorov/differential.coverage: Differential Coverage package

Description

It is a central function of all the differential.coverage package. It gets a set of intervals (noodles) as a GRanges and a list of names of bed files. Each bedfile represents a sample. For each noodle and each sample, the the sum of the lenght of intervals (read from the sample's bed file) that intersect with the noodle is returned. The result is an integer number from [0..length(noodle)] band.

Usage

count.coverage.of.noodles(noodles, bedfilnames, bed.ids = bedfilnames)

Arguments

noodles	GRanges with the intervals
bedfilnames	list of names of bedfiles, one per sample, with some (e.g. methylation) coverage information
bed.ids	optional list of names for the samples, they will be used as column names in the result. Default = bedfilnames

Value

Matrix, each row correspond to a noodle; columns are samples, sparse=TRUE

See Also

differential.coverage

favorov/differential.coverage documentation built on Feb. 18, 2022, 5:50 p.m.