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

sample_name

Integer specifiying minimum anchor length

min_anchor

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

retain_coverage

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

SGSeq is a software package for analyzing splice events from
RNA-seq data. Input data are sequence reads mapped to a reference
genome in BAM format. Genes are represented as a genome-wide
splice graph, which can be obtained from existing annotation or
can be predicted from the data. Splice events are identified
from the graph and are quantified locally using structurally
compatible reads at the start or end of each splice variant.
The package includes functions for splice event prediction,
quantification, visualization and interpretation.

getSGFeatureCountsPerSample: Compatible fragment counts for splice graph features

Description

Usage

Arguments

Value