getRandomEnrichment

getRandomEnrichment,GRanges,GRanges-method

a <code>GRanges</code> object to be overlapped with <code>query</code>

target

a <code>GRanges</code> object that will be randomly placed across the genome and overlap of these random regions with <code>target</code> will be the background distribution of association between <code>target</code> and <code>query</code>.

query

number of times the features to be shuffled

randomizations

instead of randomly placing features in <code>query</code> one can supply an already shuffled set of <code>query</code> genomic features.

rand.set

other parameters to be passed to <code>randomizeFeature</code> function. These parameters ccontrol how randomization is done.

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

A package for summary and annotation of genomic intervals. Users can visualize and 
	quantify genomic intervals over pre-defined functional regions, such as promoters, exons, 
	introns, etc. The genomic intervals represent regions with a defined chromosome position,
	which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, 
	methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal 
	information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.

getRandomEnrichment: get enrichment based on randomized feature overlap

Description

Usage

Arguments

Value

See Also

Examples