peakPermTest {ChIPpeakAnno} | R Documentation

## Permutation Test for two given peak lists

### Description

Performs a permutation test to seee if there is an association between two given peak lists.

### Usage

    peakPermTest(
      peaks1,
      peaks2,
      ntimes = 100,
      seed = as.integer(Sys.time()),
      mc.cores = getOption("mc.cores", 2L),
      maxgap = -1L,
      pool,
      TxDb,
      bindingDistribution,
      bindingType = c("TSS", "geneEnd"),
      featureType = c("transcript", "exon"),
      seqn = NA,
      ...
    )

### Arguments

`peaks1, peaks2` | an object of GRanges
`ntimes` | number of permutations
`seed` | random seed
`mc.cores` | The number of cores to use. see mclapply.
`maxgap` | See findOverlaps in the IRanges package for a description of these arguments.
`pool` | an object of permPool
`TxDb` | an object of TxDb
`bindingDistribution` | an object of bindist
`bindingType` | where the peaks should bind, TSS or geneEnd
`featureType` | what annotation type should be used for detecting the binding distribution.
`seqn` | default is NA, which means not filter the universe pool for sampling. Otherwise the universe pool will be filtered by the seqnames in seqn.
`...` | further arguments to be passed to numOverlaps.

### Value

A list of class permTestResults. See permTest

### Author(s)

Jianhong Ou

### References

Davison, A. C. and Hinkley, D. V. (1997) Bootstrap methods and their application, Cambridge University Press, United Kingdom, 156-160

### See Also

preparePool, bindist

### Examples

        path <- system.file("extdata", package="ChIPpeakAnno")
        #files <- dir(path, pattern="[12]_WS170.bed", full.names=TRUE)
        #peaks1 <- toGRanges(files[1], skip=5)
        #peaks2 <- toGRanges(files[2], skip=5)
        #peakPermTest(peaks1, peaks2, TxDb=TxDb.Celegans.UCSC.ce6.ensGene)
        if(interactive()){
            peaks1 <- toGRanges(file.path(path, "MACS2_peaks.xls"),
                                format="MACS2")
            peaks2 <- toGRanges(file.path(path, "peaks.narrowPeak"),
                                format="narrowPeak")
            library(TxDb.Hsapiens.UCSC.hg19.knownGene)
            peakPermTest(peaks1, peaks2,
                   TxDb=TxDb.Hsapiens.UCSC.hg19.knownGene, min.pctA=10)
        }

[Package ChIPpeakAnno version 3.24.2 Index]