PAS2GEF {APAlyzer} | R Documentation

## 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)

### Arguments

`GTFfile` | GTF file of gene annotation

### 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)
    	refUTRraw=PASREF$refUTRraw
        dfIPA=PASREF$dfIPA
    	dfLE=PASREF$dfLE

[Package APAlyzer version 1.6.0 Index]