topDirs {multiHiCcompare} | R 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)

[Package multiHiCcompare version 1.12.0 Index]