findSGVariants

features

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

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=1.2.2" data-mini-rdoc="SGSeq::annotateSGVariants">annotateSGVariants</a></code>.

annotate_events

Number of cores available for parallel processing

cores

Predict splice junctions and exons from BAM files and obtain
compatible read counts and FPKMs. Identify splice events and
estimate relative usage of splice variants based on compatible
read counts at event boundaries.

Leonard Goldstein

SGSeq

Splice event detection 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: Find splice variants from splice graph

Description

Usage

Arguments

Value

Examples