GTFnomencJunctionM: Junction Matrix Annotation

In harshsharma-cb/FASE: Analysis of RNA-Sequencing data using FASE (Finding Alternative Splicing Events).

Junction Matrix Annotation

Description

This function is used for correcting the annotation of junction matrix in case junction.bed files are obtained from "BAM" files using "regtools" software. This is the case where "BAM" files are downloaded some repository instead of running tophat2 pipeline. This function then produces a correctly annotated junction matrix on the basis of chromosome nomenclature as used in standard "GTF" file.

Usage

GTFnomencJunctionM(gtf, JunctionMatrix)

Arguments

gtf	gtf file of the organism.
JunctionMatrix	matrix with read counts of junctions.

Value

Annotated junction matrix file: JunctionMatix.

harshsharma-cb/FASE documentation built on Aug. 6, 2023, 1:37 a.m.