ChIPpeakAnno (version 3.6.5)

preparePool: prepare data for permutation test

Description

prepare data for permutation test peakPermTest

Usage

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.

See Also

peakPermTest, bindist

Examples

    if(interactive()){
        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")
    }