readAnnotationData: Read junctionSeq annotation files produced by QoRTs.

In JunctionSeq: JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data

Description

This function reads the "flattened" gff annotation file created by QoRTs. This annotation file contains all the gene, transcript, exon, and junction ID's and their loci. In general this function is not used by the end-user, but is called internally by runJunctionSeqAnalyses or readJunctionSeqCounts.

Usage

   readAnnotationData(flat.gff.file)

Arguments

flat.gff.file

Character string. The filename of the "flat" gff annotation file. The file may be gzip-compressed. This "flat" gff file must be produced by the QoRTs jar utility using the makeFlatGtf or mergeNovelSplices functions (depending on whether inclusion of novel splice junctions is desired).

Value

A data.frame object, containing the annotation information from the flat gff file.

Examples

gff.file <- system.file("extdata/cts/withNovel.forJunctionSeq.gff.gz",
                        package="JctSeqData");

#Parse the GFF file:
annoData <- readAnnotationData(gff.file);
head(annoData);

JunctionSeq documentation built on April 28, 2020, 7:57 p.m.