InPAS (version 1.4.4)

getUTR3eSet: 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 PDUIPDUI.log2: log2 transformed PDUI matrixshort: a matrix of usage of short formlong: a matrix of usage of long formif singleSample is TRUE, one more element, signals, will be included.

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)