preparePool

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prepare data for permutation test

prepare data for permutation test peakPermTest

Keywords
misc
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

Aliases
  • preparePool
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")
    }
Documentation reproduced from package ChIPpeakAnno, version 3.6.5, License: GPL (>= 2)

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