getUTR3eSet {InPAS} | R Documentation

## prepare dataset for test

### Description

Generate a UTR3eSet object with PDUI infomation for statistic test

### Usage

    getUTR3eSet(CPsites, coverage, genome, utr3,
                normalize=c("none", "quantiles", "quantiles.robust",
                          "mean", "median"),
                ...,
                BPPARAM=NULL, singleSample=FALSE)

### Arguments

`CPsites` | outputs of CPsites
`coverage` | coverage for each sample, outputs of coverageFromBedGraph
`genome` | an object of BSgenome
`utr3` | output of utr3Annotation
`normalize` | normalization method
`...` | parameter can be passed into normalize.quantiles.robust
`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.
`singleSample` | prepare data for singleSample analysis? default is FALSE

### Value

An object of UTR3eSet which contains following elements:

usage: an GRanges object with CP sites info.

PDUI: a matrix of PDUI

PDUI.log2: log2 transformed PDUI matrix

short: a matrix of usage of short form

long: a matrix of usage of long form

if singleSample is TRUE, one more element, signals, will be included.

### Author(s)

Jianhong Ou

### Examples

        path <- file.path(find.package("InPAS"), "extdata")
        load(file.path(path, "CPs.MAQC.rda"))
        load(file.path(path, "coverage.MAQC.rda"))
        library(BSgenome.Hsapiens.UCSC.hg19)
        data(utr3.hg19)
        getUTR3eSet(CPsites=CPs,
                     coverage=coverage,
                     genome=BSgenome.Hsapiens.UCSC.hg19,
                     utr3=utr3.hg19)

[Package InPAS version 1.18.0 Index]