overlapPermTest {regioneR} | R Documentation

## 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")

[Package regioneR version 1.16.5 Index]