perm_test {multiHiCcompare} | R Documentation |
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)
hicexp |
A Hicexp object which has been compared. |
feature |
A GRanges object contain 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. |
The permutation p-value
## Not run: data("hicexp_diff") data("hg19_cyto") perm_test(hicexp_diff, hg19_cyto) ## End(Not run)