getUTR3eSet: prepare dataset for test

Description Usage Arguments Value Author(s) Examples

View source: R/getUTR3eSet.R

Description

Generate a UTR3eSet object with PDUI infomation for statistic test

Usage

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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

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    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 April 29, 2020, 5:19 a.m.