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")
    flsall = getBamFileList()
    extpath = system.file("extdata", "mm9_REF.RData", package="APAlyzer")
    load(extpath)
    refUTRraw = refUTRraw[which(refUTRraw$Chrom=='chr19'),]
    UTRdbraw = REF3UTR(refUTRraw)
    DFUTRraw = PASEXP_3UTR(UTRdbraw, flsall, Strandtype="forward")
[Package APAlyzer version 1.0.0 Index]