RNASeqGenie (version 1.0.44)

countGenomicFeatures: Count RNA-Seq Pipeline Genomic Features

Description

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

Usage

countGenomicFeatures(gsnap_granges, genomic_features,
    parallelized=FALSE)

Arguments

gsnap_granges

GRangesList object of interval, usually where reads aligned

parallelized

Whether to count hits to genomic features in parallel (using mclapply)

Value

• A list

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), transcripts, exons, intergenic regions, and exon groups (which contain two or more exons)