REF3UTR: REF3UTR, build reference regions for 3'UTR PASs

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

REF3UTR, build reference regions for 3'UTR PASs

Description

Build 3'UTR PAS Reference for distal and proximal PAS.

Usage

    REF3UTR(refUTR)

Arguments

refUTR

a dataframe containing 6 colmuns for 3'UTR PASs: 'gene_symbol', 'Chrom', 'Strand', 'Proximal', 'Distal', 'cdsend'

Value

The function REF3UTR() returns a genomic ranges of aUTR(pPAS to dPAS) and cUTR(cdsend to pPAS) regions for each gene

Author(s)

Ruijia Wang

Examples

## build Reference ranges for 3'UTR PASs in mouse
	library(repmis)
	URL="https://github.com/RJWANGbioinfo/PAS_reference_RData/blob/master/"
	file="mm9_REF.RData"
	source_data(paste0(URL,file,"?raw=True"))
    refUTRraw=refUTRraw[which(refUTRraw$Chrom=='chr19'),]
    UTRdbraw=REF3UTR(refUTRraw)

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