REF4PAS: REF4PAS, build reference regions for 3'UTR and Intronic PAS...

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

REF4PAS, build reference regions for 3'UTR and Intronic PAS using dataframe formated input

Description

build reference regions for 3'UTR and Intronic PAS using dataframe formated input

Usage

    REF4PAS(refUTRraw, dfIPAraw, dfLEraw)

Arguments

refUTRraw	a dataframe containing 6 colmuns for 3'UTR PASs: 'gene_symbol', 'Chrom', 'Strand', 'Proximal', 'Distal', 'cdsend'
dfIPAraw	a dataframe containing 8 colmuns for Intronic PASs: 'PASid', 'gene_symbol', 'Chrom', 'Strand', 'Pos', 'upstreamSS', 'downstreamSS'. 'upstreamSS' means closest 5'/3' splice site to IPA, 'downstreamSS' means closest 3' splice site
dfLEraw	a dataframe containing 5 colmuns for 3' least exon: 'gene_symbol', 'Chrom', 'Strand', 'LEstart', 'TES'. 'LEstart' means the start position of last 3' exon.

Value

The function REF4PAS() returns list a genomic ranges of 3'UTR, Intronic PAS and last 3'exon regions for each gene

Author(s)

Ruijia Wang

Examples

## build Reference ranges for 3'UTR and Intronic PAS in mouse (mm9)
	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$Chrom=='chr19'),]
	dfIPAraw=dfIPA[which(dfIPA$Chrom=='chr19'),]
	dfLEraw=dfLE[which(dfLE$Chrom=='chr19'),]	
    PASREF=REF4PAS(refUTRraw,dfIPAraw,dfLEraw)
	UTRdbraw=PASREF$UTRdbraw
    dfIPA=PASREF$dfIPA
	dfLE=PASREF$dfLE	

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