topDirs: Filter results of multiHiCcompare

View source: R/topDirs.R

topDirsR Documentation

Filter results of multiHiCcompare

Description

Filter results of multiHiCcompare

Usage

topDirs(
  hicexp,
  logfc_cutoff = 1,
  logcpm_cutoff = 1,
  p.adj_cutoff = 0.01,
  D_cutoff = 1,
  return_df = "pairedbed",
  pval_aggregate = "max"
)

Arguments

hicexp

A hicexp object which has been compared.

logfc_cutoff

The logFC value you wish to filter by. Defaults to 1.

logcpm_cutoff

The logCPM cutoff you wish to filter by. Defaults to 1.

p.adj_cutoff

The adjusted p-value cutoff you wish to filter by. Defaults to 0.01.

D_cutoff

The distance cutoff you wish to filter by. Interactions with a D < D_cutoff will be filtered. Defaults to 1.

return_df

The format for the data.frame returned by the function. Options are "bed" and "pairedbed" (Default).

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

Details

This function is meant to filter the results of multiHiCcompare. The top differentially interacting regions (DIRs) can be returned by using this function. When the return_df = "bed" option is set the resulting data.frame can be input into the plot_pvals or plot_counts functions to visualize the top DIRs.

Value

A data.table containing the filtered results.

Examples

data('hicexp_diff')
topDirs(hicexp_diff)

dozmorovlab/multiHiCcompare documentation built on April 23, 2022, 9:56 a.m.