getRandomEnrichment-methods: get enrichment based on randomized feature overlap

Description Usage Arguments Value See Also Examples

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

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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

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

BIMSBbioinfo/genomation documentation built on Feb. 4, 2018, 12:11 p.m.