R: get enrichment based on randomized feature overlap

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

Examples

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