Perform a permutation test to check enrichment of a genomic feature with DIRs detected by multiHiCcompare

perm_test(
  hicexp,
  feature,
  p.adj_cutoff = 10^-10,
  logfc_cutoff = 1,
  num.perm = 1000,
  pval_aggregate = "max"
)

Arguments

hicexp	A Hicexp object which has been compared.
feature	A GRanges object containing locations for a genomic feature you would like to test for enrichment in the differentially interacting regions (DIRs).
p.adj_cutoff	The adjusted p-value cutoff for declaring a region significant. See ?topDirs for more information. Defaults to 10^-10
logfc_cutoff	The log fold change cutoff for a region to be declared significant. See ?topDirs for more information. Defaults to 1.
num.perm	The number of permutations to run. Defaults to 1000.
pval_aggregate	Method to aggregate region-specific p-values. If a region differentially interacts with several other regions, the p-values are aggregated using a 'max' method (Default, select maximum p-value, most conservative), or the Fisher ('fisher'), Lancaster ('lancaster'), or Sidak ('sidak') methods (see 'aggregate' package). regions, it is assigned a single p-value aggregated from several. See ?topDirs

The permutation p-value

if (FALSE) {
data("hicexp_diff")
data("hg19_cyto")
perm_test(hicexp_diff, hg19_cyto)
}