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, alpha = 0.05,
      return_df = "pairedbed")

### 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.
`alpha` | The p-value cutoff for determining the count of number of times a region is significant. Used to calculate the number of times a region was detected as significantly interacting. Defaults to 0.05.
`return_df` | The format for the data.frame returned by the function. Options are "bed" and "pairedbed".

### 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 1.5.0 Index]