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

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

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	

APAlyzer documentation built on Nov. 8, 2020, 4:54 p.m.