Brick_load_data_from_mcool {HiCBricks}R Documentation

Load a NxN dimensional matrix into the Brick store from an mcool file.

Description

Read an mcool contact matrix coming out of 4D nucleome projects into a Brick store.

Usage

Brick_load_data_from_mcool(Brick, mcool, chr1, chr2, binsize = NULL,
    cooler.batch.size = 1e+06, matrix.chunk = 2000,
    dont.look.for.chr2 = FALSE, remove.prior = FALSE,
    norm.factor = "Iterative-Correction")

Arguments

Brick

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

mcool

Required. Path to an mcool file.

chr1

Required. A character vector of length 1 specifying the chromosome corresponding to the rows of the matrix

chr2

Required. A character vector of length 1 specifying the chromosome corresponding to the columns of the matrix

binsize

Optional. The binsize to select from an mcool file.

cooler.batch.size

Optional. Default 1000000. The number of values to read per iteration through a mcool file.

matrix.chunk

Optional. Default 2000. The nxn matrix square to fill per iteration in a mcool file.

dont.look.for.chr2

Required. At startup, the function will attempt to search for the first occurence of a chr2 contact value. This is done to avoid the reading of all chr1 values for every chunk processed. If chr1 and chr2 are equivalent, consider setting it to FALSE.

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.

norm.factor

Optional. Default "Iterative-Correction". The normalization factor to use for normalization from an mcool file. norm.factor currently accepts one of "Iterative-Correction", "Knight-Ruitz", "Vanilla-coverage", "Vanilla-coverage-square-root" and NULL. If NULL, the function will load only counts from the mcool file.

Value

Returns TRUE if all went well.

See Also

CreateBrick_from_mcool to create matrix from an mcool file, Brick_list_mcool_resolutions to list available resolutions in an mcool file, Brick_list_mcool_normalisations to list available normalisation factors in the mcool file.

Examples


## Not run: 

require(curl)
curl_download(url = paste("https://data.4dnucleome.org/"
"files-processed/4DNFI7JNCNFB/"
"@download/4DNFI7JNCNFB.mcool",sep = ""),
destfile = file.path(tempdir(),"H1-hESC-HiC-4DNFI7JNCNFB.mcool"))

Output.brick <- file.path(tempdir(), 
 "H1-hESC-HiC-4DNFI7JNCNFB-10000-ICE-normalised-chr1.brick")
mcool <- file.path(tempdir(),"H1-hESC-HiC-4DNFI7JNCNFB.mcool")

CreateBrick_from_mcool(Brick = Output.brick,
mcool = mcool,
binsize = 10000,
chrs = "chr1")

Brick_load_data_from_mcool(Brick = Output.brick, mcool = mcool,
chr1 = "chr1", chr2 = "chr1", binsize = 10000,
cooler.batch.size = 1000000, matrix.chunk = 2000,
dont.look.for.chr2 = TRUE, remove.prior = TRUE,
norm.factor = "Iterative-Correction")


## End(Not run)



[Package HiCBricks version 1.2.0 Index]