perm_test: Perform a permutation test to check enrichment of a genomic...

In multiHiCcompare: Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

Description

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

Usage

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

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.

Value

The permutation p-value

Examples

## Not run: 
data("hicexp_diff")
data("hg19_cyto")
perm_test(hicexp_diff, hg19_cyto)

## End(Not run)

multiHiCcompare documentation built on Nov. 8, 2020, 7:04 p.m.