findTxVariants

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
transcript variants should be annotated in terms of canonical events.
For details see help page for <code><a rd-options="" href="/link/annotateTxVariants?package=SGSeq&version=1.0.6" data-mini-rdoc="SGSeq::annotateTxVariants">annotateTxVariants</a></code>.

annotate_events

Number of cores available for parallel processing

cores


Find transcript variants from splice graph


RNA-seq data are informative for the analysis of known and
novel transcript isoforms. While the short length of RNA-seq
reads limits the ability to predict and quantify full-length
transcripts, short read data are well suited for the analysis
of individual alternative transcripts events (e.g. inclusion
or skipping of a cassette exon). The SGSeq package enables the
prediction, quantification and visualization of alternative
transcript events from BAM files.

Leonard Goldstein

SGSeq

Prediction, quantification and visualization of alternative
transcript events from RNA-seq data

findTxVariants function

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

findTxVariants: Find transcript variants from splice graph

Description

Usage

Arguments

Value

Examples