regioneR (version 1.4.0)

overlapPermTest: Permutation Test for Overlap

Description

Performs a permutation test to see if there is an association in overlap between a region set A and a region set B creating random regions through the genome.

Usage

overlapPermTest (A, B, alternative="auto", ...)

Arguments

A

a region set in any of the accepted formats by toGRanges (GenomicRanges, data.frame, etc...)

B

a region set in any of the accepted formats by toGRanges (GenomicRanges, data.frame, etc...)

alternative

the alternative hypothesis must be one of "greater", "less" or "auto". If "auto", the alternative will be decided depending on the data.

...

further arguments to be passed to or from methods.

Value

A list of class permTestResults containing the following components:

• pval the p-value of the test.
• ntimes the number of permutations.
• alternative a character string describing the alternative hypotesis.
• observed the value of the statistic for the original data set.
• permuted the values of the statistic for each permuted data set.
• zscore the value of the standard score. (observed-mean(permuted))/sd(permuted)

See Also

overlapGraphicalSummary, overlapRegions, toDataframe, toGRanges, permTest

Examples

genome <- filterChromosomes(getGenome("hg19"), keep.chr="chr1")
A <- createRandomRegions(nregions=20, length.mean=10000000, length.sd=20000, genome=genome, non.overlapping=FALSE) 
B <- c(A, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE))

pt <- overlapPermTest(A=A, B=B, ntimes=10, genome=genome, non.overlapping=FALSE, verbose=TRUE)
summary(pt)
plot(pt)
plot(pt, plotType="Tailed")