analyzeVariants

object

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

Number of cores available for parallel processing

cores


High-level function for the analysis of transcript variants from
splice graph features. Transcript variants are identified with
<code><a rd-options="" href="/link/findTxVariants?package=SGSeq&version=1.0.6" data-mini-rdoc="SGSeq::findTxVariants">findTxVariants</a></code>. Representative counts and estimated
variant frequencies are obtained with <code><a rd-options="" href="/link/getTxVariantCounts?package=SGSeq&version=1.0.6" data-mini-rdoc="SGSeq::getTxVariantCounts">getTxVariantCounts</a></code>.


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

analyzeVariants function


High-level function for the analysis of transcript variants from
splice graph features. Transcript variants are identified with
<code><a rd-options='' href='findTxVariants'>findTxVariants</a></code>. Representative counts and estimated
variant frequencies are obtained with <code><a rd-options='' href='getTxVariantCounts'>getTxVariantCounts</a></code>.


analyzeVariants: Analysis of transcript variants

Description

Usage

Arguments

Value

Examples