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 splice variants from
splice graph features. Splice variants are identified with
<code><a rd-options="" href="/link/findSGVariants?package=SGSeq&version=1.2.2" data-mini-rdoc="SGSeq::findSGVariants">findSGVariants</a></code>. Representative counts are obtained
and variant frequencies estimated with <code><a rd-options="" href="/link/getSGVariantCounts?package=SGSeq&version=1.2.2" data-mini-rdoc="SGSeq::getSGVariantCounts">getSGVariantCounts</a></code>.


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

analyzeVariants function


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


analyzeVariants: Analysis of splice variants

Description

Usage

Arguments

Value

Examples