RNASeqGenie (version 1.0.44)

detectNcRNA: Detect ncRNA Read Hits

Description

Determines how many ncRNA regions were hit and how many reads hit this genomic feature. These calculations are also performed on the non-genic subset of the ncRNA regions

Usage

detectNcRNA(gsnap_granges, genomic_features, options)

Arguments

gsnap_granges

A set of alignments stored as a GRangesList

genomic_features

A list that must have a "genes" element that is a GRangesList of genic regions

options

An options object as created by HTSeqGenieBase

Value

• A list of the number of hits to each ncRNA region as well as the number of reads mapping to this region