getRandomEnrichment {genomation} | R Documentation

## get enrichment based on randomized feature overlap

### Description

This function measures the association between two genomic features by randomizing one feature and counting the overlaps in randomized sets. That is to say, `query` feature will be randomly distributed over the genome (constrained by provided options), and the overlap of `target` with these randomized features will be measured.

### Usage

    getRandomEnrichment(target, query, randomizations = 1000, rand.set = NULL,
      ...)

    ## S4 method for signature 'GRanges,GRanges'
    getRandomEnrichment(target, query,
      randomizations = 1000, rand.set = NULL, ...)

### Arguments

`target` | a `GRanges` object to be overlapped with `query`
`query` | a `GRanges` object that will be randomly placed across the genome and overlap of these random regions with `target` will be the background distribution of association between `target` and `query`.
`randomizations` | number of times the features to be shuffled
`rand.set` | instead of randomly placing features in `query` one can supply an already shuffled set of `query` genomic features.
`...` | other parameters to be passed to `randomizeFeature` function. These parameters ccontrol how randomization is done.

### Value

returns a `RandomEnrichment` object

### See Also

`randomizeFeature`

### Examples

    data(cage)
    data(cpgi)

    enr = getRandomEnrichment(cage, cpgi, randomizations=50)

[Package genomation version 1.12.0 Index]