utr3UsageEstimation {InPAS} | R Documentation

## 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

### 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)
        }

[Package InPAS version 1.14.2 Index]