countFromBed: Count from beds to make count matrix

In kathrynrozengagnon/CLIPflexR: CLIP tools and wrappers in R

Count from beds to make count matrix

Description

Count from beds to make count matrix

Usage

countFromBed(Bed, GR, notStranded = TRUE, interFeature = FALSE)

Arguments

Bed	BED bed files containing mapped reads.
GR	genomic ranges object over which to count.
notStranded	if strand information should be considered when counting, TRUE (ignore strand) or FALSE (consider strand; default).
interFeature	discard reads mapping to multiple features, TRUE or FALSE (default).

Value

count matrix.

Author(s)

Kathryn Rozen-Gagnon

Examples

testFasta <- system.file("extdata/hg19Small.fa",package="CLIPflexR")
myIndex <-suppressWarnings(bowtie2_index(testFasta, overwrite = TRUE))

kathrynrozengagnon/CLIPflexR documentation built on Dec. 8, 2022, 7:31 p.m.