max.peak.score.for.each.noodle: max.peak.score.for.each.noodle

In favorov/differential.coverage: Differential Coverage package

Description

Could be an alterantive 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 maximal score of a peak that intersect this noodle in the sample, if any, or 0 othewise, is returned. Supposed to called for annotation of a few selected noodles.

Usage

## S3 method for class 'peak.score.for.each.noodle'
max(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, value=max(score) or 0

See Also

differential.coverage

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