test.enrichment {chicane}

test.enrichment

Description

test.enrichment

Usage

test.enrichment(
  interaction.data,
  feature.bed,
  significance.cutoff = 0.05,
  span = 0,
  n = 1000,
  remove.bait.to.bait = TRUE
)

Arguments

interaction.data

Data table containing details on interactions

feature.bed

BED file with regions of features

significance.cutoff

q-value threshold for significant interactions

span

Distance around target restriction fragment to consider. If set to zero (default), only features that overlap with the restriction fragment itself are considered.

n

Number of random samples to consider

remove.bait.to.bait

Logical specifying whether to exclude bait-to-bait interactions

Value

list with elements

observed

observed overlap between significant interactions and features

random

vector of length n giving overlap between random samples and features

Author(s)

Erle Holgersen <[e-mail]>

Examples

if( bedtools.installed() ) {
  data(bre80);
  ctcf.bed <- system.file('extdata', 'T47D_chr2_CTCF.bed.gz', package = 'chicane');

  results <- chicane(interactions = bre80);
  test.enrichment(results, ctcf.bed, significance.cutoff = 0.25);
}