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HTSeqGenie (version 4.2.0)

countFeatures: Count RNA-Seq Pipeline Genomic Features

Description

Given GRanges, counts number of hits by gene, exon, intergenic, etc

Usage

countFeatures(reads, features)

Arguments

reads
GRangesList object of interval, usually where reads aligned
features
A list of genome annotations as GRangesList

Value

A list of counts by feature

Details

Given a GRanges object, this function performs an overlap against a previously created set of genomic regions. These genomic regions include genes, coding portions of genes (CDS), exons, intergenic regions, and exon groups (which contain two or more exons)