perm_test {multiHiCcompare} | R Documentation

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

### 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,
      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

### Value

The permutation p-value

### Examples

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

    ## End(Not run)

[Package multiHiCcompare version 1.12.0 Index]