getSGFeatureCountsPerSample

features

BAM file with genomic RNA-seq read alignments

file_bam

Logical, <code>TRUE</code> for paired-end data,
<code>FALSE</code> for single-end data

paired_end

Logical indicating whether coverages for each
exon should be retained as an <code>IntegerList</code> in elementMetadata
column &#147;coverage&#148;. This allows filtering of features
using more stringent criteria after the initial prediction.

retain_coverage

sample_name

If <code>TRUE</code>, generate messages indicating progress

verbose

Number of cores available for parallel processing

cores


Obtain counts of compatible fragments for splice graph features.


internal

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.

getSGFeatureCountsPerSample: Compatible fragment counts for splice graph features

Description

Usage

Arguments

Value