getSGFeatureCounts

<code>data.frame</code> with sample information.
Required columns are &#147;sample_name&#148;, &#147;file_bam&#148;,
&#147;paired_end&#148;, &#147;read_length&#148;, &#147;frag_length&#148;
and &#147;lib_size&#148;. Alignment information can be obtained with
function <code>getBamInfo</code>.

sample_info

features

cores_per_sample

<code>BiocParallelParam</code> for processing samples in parallel,
defaults to <code>MulticoreParam(1)</code>

BPPARAM


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


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.

getSGFeatureCounts: Compatible counts for splice graph features from BAM files

Description

Usage

Arguments

Value

Examples