exportJuicebox {multiHiCcompare} | R Documentation

## Export multiHiCcompare results for visualization in Juicebox

### Description

Export multiHiCcompare results for visualization in Juicebox

### Usage

    exportJuicebox(hicexp, logfc_cutoff = 1, logcpm_cutoff = 1,
      p.adj_cutoff = 0.01, D_cutoff = 1,
      file_name = "juiceboxAnnotations.txt", color = "0,0,255")

### 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.
`file_name` | The file name of the text file to be saved.
`color` | A decimal RGB color code. Should be a character value in form of "0,0,255". Defaults to color code for blue. This will determine the color of the annotations on the Juicebox heatmap.

### Details

This function is meant to filter the results of multiHiCcompare and export the significant differentially interacting regions into a text file which can be imported into Juicebox as a 2D annotations file. This will allow you to visualize where your DIRs occur on the heatmap of the interactions. Please see the included vignette on using Juicebox to visualize multiHiCcompare results. This can be accessed with browseVignettes("multiHiCcompare").

### Value

A text file containing annotations for input into Juicebox.

### Examples

    data('hicexp_diff')
    exportJuicebox(hicexp_diff, file_name = "juiceboxAnnotations.txt")

[Package multiHiCcompare version 1.4.0 Index]