Description Usage Arguments Value Author(s) See Also Examples
prepare data for permutation test peakPermTest
1 2 3 4 5 6 7 8 | preparePool(
TxDb,
template,
bindingDistribution,
bindingType = c("TSS", "geneEnd"),
featureType = c("transcript", "exon"),
seqn = NA
)
|
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. |
a list with two elements, grs, a list of GRanges. N, the numbers of elements should be drawn from in each GRanges.
Jianhong Ou
peakPermTest, bindist
1 2 3 4 5 6 7 8 9 10 | 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")
}
|
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