getUTR3eSet: prepare dataset for test

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

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)

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