PAS2GEF: PAS2GEF, build reference regions for 3'UTR PASs

In RJWANGbioinfo/APAlyzer: A toolkit for APA analysis using RNA-seq data

PAS2GEF, build reference regions for 3'UTR PASs

Description

Build 3'UTR PAS and IPA (IPA and LE) Reference using GTF file.

Usage

    PAS2GEF(GTFfile,AnnoMethod="V2")

Arguments

GTFfile	GTF file of gene annotation
AnnoMethod	annotation method used to build PAS reference, either 'legacy' or 'V2', default is 'V2'

Value

The function PAS2GEF() returns 3 input tables of PAS references: PASREF$refUTRraw is for 3'UTR PAS, PASREF$dfIPA and PASREF$dfLE are for IPA references.

Author(s)

Ruijia Wang

Examples

## build Reference ranges for 3'UTR PASs in mouse
	download.file(url='ftp://ftp.ensembl.org/pub/release-99/gtf/mus_musculus/Mus_musculus.GRCm38.99.gtf.gz',
              destfile='Mus_musculus.GRCm38.99.gtf.gz')			  
	GTFfile="Mus_musculus.GRCm38.99.gtf.gz"	

	PASREF=PAS2GEF(GTFfile, AnnoMethod="V2")	
	refUTRraw=PASREF$refUTRraw
    dfIPA=PASREF$dfIPA
	dfLE=PASREF$dfLE
	

RJWANGbioinfo/APAlyzer documentation built on Dec. 6, 2024, 3:36 p.m.