Description Usage Arguments Value Examples
Perform a permutation test to check enrichment of a genomic feature with DIRs detected by multiHiCcompare
1 2 3 4 5 6 7 8 |
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
1 2 3 4 5 6 | ## Not run:
data("hicexp_diff")
data("hg19_cyto")
perm_test(hicexp_diff, hg19_cyto)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.