overlapPermTest {regioneR} | R Documentation

## Permutation Test for Overlap

### Description

Performs a permutation test to see if the overlap between two sets of regions A and B is higher (or lower) than expected by chance. It will internally call `permTest` with the appropiate parameters to perform the permutation test. If B is a list or a GRangesList, it will perform one permutation test per element of the list, testing the overlap between A and each element of B independently.

### 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)`

### Note

IMPORTANT: Since it uses `link{permTest}` internally, it is possible to use most of the parameters of that function in `overlapPermTest`, including: `ntimes`, `force.parallel`, `min.parallel` and `verbose`. In addition, this function accepts most parameters of the `randomizeRegions` function including `genome`, `mask`, `allow.overlaps` and `per.chromosome` and the parameters of `numOverlaps` such as `count.once`.

### 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")

    C <- c(B, createRandomRegions(nregions=10, length.mean=10000, length.sd=20000, genome=genome, non.overlapping=FALSE))
    pt <- overlapPermTest(A=A, B=list(B=B, C=C), ntimes=10, genome=genome, non.overlapping=FALSE, verbose=TRUE)
    summary(pt)
    plot(pt)

[Package regioneR version 1.24.0 Index]