PASEXP_3UTR: PASEXP_3UTR, calculate relative expression of aUTR and cUTR...

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

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")

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