exportJuicebox: Export multiHiCcompare results for visualization in Juicebox

In dozmorovlab/multHiCcompare: Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

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") 

dozmorovlab/multHiCcompare documentation built on April 30, 2022, 3:02 p.m.