PASEXP_3UTR {APAlyzer} | R Documentation

## PASEXP_3UTR, calculate relative expression of aUTR and cUTR regions

### Description

Map reads to 3'UTR APA regions and calculate relative expression of aUTR and cUTR regions.

### Usage

        PASEXP_3UTR(UTRdb, flS, Strandtype="NONE")

### Arguments

`UTRdb` | a genomic ranges of aUTR(pPAS to dPAS) and cUTR(cdsend to pPAS) regions for each gene
`flS` | bamfile lists containing the file and path of bam files
`Strandtype` | strand type of the bam file; "forward" is forwand sequencing, "invert" is reverse sequencing and "NONE" is non-strand specific, Default is "NONE".

### Value

The function `PASEXP_3UTR()` return a dataframe containning reads count, RPKM and relative expression of aUTR and cUTR for each gene

### Author(s)

Ruijia Wang

### Examples

    ## count reads mapped to 3'UTR APA regions and
    ## calculate relative expression of aUTR and cUTR regions
    ## using forward sequencing
        library("TBX20BamSubset")
        library("Rsamtools")
        library("GenomicAlignments")
    	library("repmis")
        flsall = getBamFileList()
    	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)
        DFUTRraw = PASEXP_3UTR(UTRdbraw, flsall, Strandtype="forward")

[Package APAlyzer version 1.1.2 Index]