preparePool: prepare data for permutation test

Description Usage Arguments Value Author(s) See Also Examples

View source: R/preparePool.R

Description

prepare data for permutation test peakPermTest

Usage

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preparePool(
  TxDb,
  template,
  bindingDistribution,
  bindingType = c("TSS", "geneEnd"),
  featureType = c("transcript", "exon"),
  seqn = NA
)

Arguments

TxDb

an object of TxDb

template

an object of GRanges

bindingDistribution

an object of bindist

bindingType

the relevant position to features

featureType

feature type, transcript or exon.

seqn

seqnames. If given, the pool for permutation will be restrict in the given chromosomes.

Value

a list with two elements, grs, a list of GRanges. N, the numbers of elements should be drawn from in each GRanges.

Author(s)

Jianhong Ou

See Also

peakPermTest, bindist

Examples

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    if(interactive() || Sys.getenv("USER")=="jianhongou"){
        path <- system.file("extdata", package="ChIPpeakAnno")
        peaksA <- toGRanges(file.path(path, "peaks.narrowPeak"), 
                            format="narrowPeak")
        peaksB <- toGRanges(file.path(path, "MACS2_peaks.xls"), format="MACS2")
        library(TxDb.Hsapiens.UCSC.hg19.knownGene)
        ppp <- preparePool(TxDb.Hsapiens.UCSC.hg19.knownGene, 
                           peaksA, bindingType="TSS",
                           featureType="transcript")
    }

ChIPpeakAnno documentation built on April 1, 2021, 6:01 p.m.