Brick_call_compartments {HiCBricks}R Documentation

Identify compartments in the Hi-C data

Description

Brick_call_compartments identifies compartments in Hi-C data. Reference Lieberman-Aiden et al. 2009.

Usage

Brick_call_compartments(Brick, chr, resolution)

Arguments

Brick

Required. A string specifying the path to the Brick store created with Create_many_Brick.

chr

Required. A string specifying the chromosome for the cis Hi-C matrix from which values will be retrieved at a certain distance.

resolution

Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed

Value

A dataframe containing the chromosome genomic coordinates and the first three principal components.

Examples

Bintable.path <- system.file(file.path("extdata", "Bintable_100kb.bins"), 
package = "HiCBricks")

out_dir <- file.path(tempdir(), "get_vector_val_test")
dir.create(out_dir)

My_BrickContainer <- Create_many_Bricks(BinTable = Bintable.path, 
  bin_delim = " ", output_directory = out_dir, file_prefix = "Test",
  experiment_name = "Vignette Test", resolution = 100000,
  remove_existing = TRUE)

Matrix_file <- system.file(file.path("extdata", 
"Sexton2012_yaffetanay_CisTrans_100000_corrected_chr2L.txt.gz"), 
package = "HiCBricks")

Brick_load_matrix(Brick = My_BrickContainer, chr1 = "chr2L", 
chr2 = "chr2L", matrix_file = Matrix_file, delim = " ", 
remove_prior = TRUE, resolution = 100000)

Brick_call_compartments(Brick = My_BrickContainer, chr = "chr2L",
resolution = 100000)


[Package HiCBricks version 1.4.0 Index]