findSGVariants

features

If more than <code>maxnvariant</code> variants are
identified in an event, the event is skipped, resulting in a warning.
Set to <code>NA</code> to include all events.

maxnvariant

Logical indicating whether identified
splice variants should be annotated in terms of canonical events.
For details see help page for <code><a rd-options="" href="/link/annotateSGVariants?package=SGSeq&version=1.6.5" data-mini-rdoc="SGSeq::annotateSGVariants">annotateSGVariants</a></code>.

annotate_events

Character string indicating whether identified splice
variants should be filtered. Possible options are &#147;default&#148;
(only include variants for events with all variants closed),
&#147;closed&#148; (only include closed variants) and &#147;all&#148;
(include all variants).

include

Number of cores available for parallel processing

cores


Identify splice variants from splice graph.


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.

Leonard Goldstein

SGSeq

Splice event prediction and quantification from RNA-seq data

findSGVariants function

Logical indicating whether identified
splice variants should be annotated in terms of canonical events.
For details see help page for <code><a rd-options='' href='annotateSGVariants'>annotateSGVariants</a></code>.

findSGVariants: Identify splice variants from splice graph

Description

Usage

Arguments

Value

Examples