getSGFeatureCounts

Data frame with sample information.
Required columns are <dquote>sample_name</dquote>, <dquote>file_bam</dquote>,
<dquote>paired_end</dquote>, <dquote>read_length</dquote>, <dquote>frag_length</dquote>
and <dquote>lib_size</dquote>. Library information can be obtained with
function <code>getBamInfo</code>.

sample_info

features

Integer specifiying minimum anchor length

min_anchor

Logical indicating only counts should be returned

counts_only

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

verbose

Number of cores available for parallel processing

cores

Compatible counts are obtained for each sample and combined into
an <code>SGFeatureCounts</code> object.

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.

Leonard Goldstein

SGSeq

Splice event prediction and quantification from RNA-seq data

getSGFeatureCounts function

Data frame with sample information.
Required columns are <dQuote>sample_name</dQuote>, <dQuote>file_bam</dQuote>,
<dQuote>paired_end</dQuote>, <dQuote>read_length</dQuote>, <dQuote>frag_length</dQuote>
and <dQuote>lib_size</dQuote>. Library information can be obtained with
function <code>getBamInfo</code>.

getSGFeatureCounts: Compatible counts for splice graph features from BAM files

Description

Usage

Arguments

Value

Examples