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

Description Usage Arguments Value See Also

View source: R/noodles.coverage.R

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

1
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.