utr3UsageEstimation: estimation of 3'UTR usage for each region

In InPAS: InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

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

Author(s)

Jianhong Ou

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)
    }

InPAS documentation built on Nov. 8, 2020, 5:03 p.m.