REF4PAS {APAlyzer} | R Documentation

## 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

[Package APAlyzer version 1.6.0 Index]