InPAS (version 1.4.4)

utr3UsageEstimation: estimation of 3'UTR usage for each region

Description

estimation of 3'UTR usage for short form and long form

Usage

utr3UsageEstimation(CPsites, coverage, genome, utr3,  gp1, gp2=NULL,  short_coverage_threshold = 10,  long_coverage_threshold = 2,  adjusted.P_val.cutoff = 0.05,  dPDUI_cutoff = 0.3,  PDUI_logFC_cutoff=0.59, BPPARAM=NULL)

Arguments

CPsites

outputs of CPsites

coverage

coverage for each sample, outputs of coverageFromBedGraph

genome

an object of BSgenome

utr3

output of utr3Annotation

gp1

tag names involved in group 1

gp2

tag names involved in group 2

short_coverage_threshold

cutoff threshold for coverage in thre region of short form

long_coverage_threshold

cutoff threshold for coverage in thre region of long form

adjusted.P_val.cutoff

cutoff value for adjusted p.value

dPDUI_cutoff

cutoff value for differenctial PAS(polyadenylation signal) usage index

PDUI_logFC_cutoff

cutoff value for log2 fold change of PAS(polyadenylation signal) usage index

BPPARAM

An optional BiocParallelParam instance determining the parallel back-end to be used during evaluation, or a list of BiocParallelParam instances, to be applied in sequence for nested calls to bplapply.

Value

return an object of GRanges

Examples

    if(interactive()){
        library(BSgenome.Mmusculus.UCSC.mm10)
        path <- file.path(find.package("InPAS"), "extdata")
        bedgraphs <- file.path(path, "Baf3.extract.bedgraph")
        data(utr3.mm10)
        tags <- "Baf3"
        genome <- BSgenome.Mmusculus.UCSC.mm10
        coverage <- 
            coverageFromBedGraph(bedgraphs, tags, genome, hugeData=FALSE)
        CP <- CPsites(coverage=coverage, gp1=tags, gp2=NULL, genome=genome, 
            utr3=utr3.mm10, coverage_threshold=5, long_coverage_threshold=5)
        res <- utr3UsageEstimation(CP, coverage, 
            utr3.mm10, genome, gp1=tags, gp2=NULL)
    }