predictTxFeaturesRanges

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

<code>GRanges</code> of genomic regions to be considered for
feature prediction, passed to <code>ScanBamParam</code>

which

Minimum fragment count required for a splice
junction to be included. If specified, argument <code>alpha</code> is ignored.

min_junction_count

Minimum splice frequency required for a splice junction
to be included

Minimum relative coverage required for an internal exon
to be included

beta

Minimum relative coverage required for a terminal exon
to be included

gamma

Logical indicating whether counts of
compatible fragments should be included in elementMetadata column
&#147;N&#148;

include_counts

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

Logical indicating whether predictions
should be limited to identification of splice junctions only

junctions_only


Identification of splice junctions and exons for a given
  chromosome and strand


internal

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.

predictTxFeaturesRanges: Identification of splice junctions and exons for a given chromosome and strand

Description

Usage

Arguments

Value