splicesiteOverlap

splicesites

Character vector indicating whether the spliced boundary
is to the left (&#147;L&#148;) or right (&#147;R&#148;) of the splice site

side

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

frag_exonic

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

frag_intron

Integer specifiying minimum anchor length

min_anchor

Character string indicating whether considered fragments
should be all that overlap the splice site (&#147;all&#148;), those
that are spliced at the site (&#147;spliced&#148;) or those that are
not spliced, i.e. extend into the adjacent intron (&#147;unspliced&#148;)

include

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

counts


Identify fragments with alignments extending across exon/intron boundaries.


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.

splicesiteOverlap: Compatible fragment counts for splice sites

Description

Usage

Arguments

Value