peakPermTest: Permutation Test for two given peak lists

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

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)
    }

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