| peakPermTest {ChIPpeakAnno} | R Documentation |
Performs a permutation test to seee if there is an association between two given peak lists.
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, ...)
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. |
A list of class permTestResults. See permTest
Jianhong Ou
Davison, A. C. and Hinkley, D. V. (1997) Bootstrap methods and their application, Cambridge University Press, United Kingdom, 156-160
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)
}