exonCompatible

exons

Logical vector indicating whether LHS boundary is spliced

spliceL

Logical vector indicating whether RHS boundary is spliced

spliceR

<code>IRangesList</code> of exonic regions, one entry
per fragment

frag_exonic

<code>IRangesList</code> of introns, one entry per fragment

frag_intron

Logical indicating whether counts or indices of
compatible fragments should be returned

counts

Identify fragments compatible with exons.

internal

SGSeq is a software package for analyzing splice events from
	     RNA-seq data. Input data are sequence reads mapped to a reference
	     genome in BAM format. Genes are represented as a genome-wide
	     splice graph, which can be obtained from existing annotation or
	     can be predicted from the data. Splice events are identified
	     from the graph and are quantified locally using structurally
	     compatible reads at the start or end of each splice variant.
	     The package includes functions for splice event prediction,
	     quantification, visualization and interpretation.

exonCompatible: Compatible fragment counts for exons

Description

Usage

Arguments

Value