Brick_load_data_from_sparse: Identify compartments in the Hi-C data

Description Usage Arguments Value Examples

View source: R/Brick_functions.R

Description

Brick_load_data_from_sparse loads data from a table like file, such as sparse matrices.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
Brick_load_data_from_sparse(
    Brick,
    table_file,
    delim = " ",
    resolution = NULL,
    batch_size = 1e+06,
    matrix_chunk = 2000,
    col_index = c(1, 2, 3),
    remove_prior = FALSE
)

Arguments

Brick

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

table_file

Path to the file that will be loaded

delim

Optional. Default " " The delimiter of the matrix file.

resolution

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

batch_size

Optional Default 1000000 Number of rows to read with each iteration from a sparse matrix.

matrix_chunk

Optional Default 2000 The nxn matrix square to fill per iteration to a Brick object.

col_index

Optional. Default "c(1,2,3)". A character vector of length 3 containing the indexes of the required columns in the table file. the first index, corresponds to bin1, the second to bin2 and the third to the signal value.

remove_prior

Optional. Default FALSE If a matrix was loaded before, it will not be replaced. Use remove_prior to override and replace the existing matrix.

Value

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

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
## Not run: 
Bintable.path <- system.file(file.path("extdata", "Bintable_100kb.bins"), 
package = "HiCBricks")

out_dir <- file.path(tempdir(), "get_vector_val_test")
if(!file.exists(out_dir)){
    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_export_to_sparse(Brick = My_BrickContainer, 
out_file = file.path(out_dir, "example_out.txt"), 
remove_file = TRUE, sep = " ", 
resolution = 100000)

Brick_load_data_from_sparse(Brick = My_BrickContainer, 
table_file = file.path(out_dir, "example_out.txt"), 
delim = " ", resolution = 100000, col_index = c(3,4,5))
    

## End(Not run)

koustav-pal/HiCBlocks documentation built on Jan. 6, 2022, 2:36 a.m.