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) }