countFeatures: Count RNA-Seq Pipeline Genomic Features

Description Usage Arguments Details Value Author(s)

View source: R/countGenomicFeatures.R

Description

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

Usage

1
countFeatures(reads, features)

Arguments

reads

GRangesList object of interval, usually where reads aligned

features

A list of genome annotations as GRangesList

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)

Value

A list of counts by feature

Author(s)

Cory Barr


HTSeqGenie documentation built on Nov. 8, 2020, 6:12 p.m.