preparePool: prepare data for permutation test

In jianhong/ChIPpeakAnno: Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

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.

Author(s)

Jianhong Ou

See Also

peakPermTest, bindist

Examples

    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")
    }

jianhong/ChIPpeakAnno documentation built on Nov. 1, 2024, 8:55 a.m.