View source: R/Brick_functions.R
Brick_load_data_from_mcool | R Documentation |
Read an mcool contact matrix coming out of 4D nucleome projects into a Brick store.
Brick_load_data_from_mcool( Brick, mcool, resolution = NULL, matrix_chunk = 2000, cooler_read_limit = 1e+07, remove_prior = FALSE, norm_factor = "Iterative-Correction" )
Brick |
Required. A string specifying the path to the Brick store created with Create_many_Brick. |
mcool |
Required. Path to an mcool file. |
resolution |
Optional. Default NA When an object of class BrickContainer is provided, resolution defines the resolution on which the function is executed |
matrix_chunk |
Optional. Default 2000. The nxn matrix square to fill per iteration in a mcool file. |
cooler_read_limit |
Optional. Default 10000000. cooler_read_limit sets the upper limit for the number of records per matrix chunk. If the number of records per chunk is higher than this value, the matrix_chunk value will be re-evaluated dynamically. |
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. |
Returns TRUE if all went well.
Create_many_Bricks_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.
## Not run: require(curl) out_dir <- file.path(tempdir(),"mcool_load_test") dir.create(path = out_dir) curl_download(url = paste("https://data.4dnucleome.org/", "files-processed/4DNFI7JNCNFB/", "@download/4DNFI7JNCNFB.mcool", sep = ""), destfile = file.path(out_dir,"H1-hESC-HiC-4DNFI7JNCNFB.mcool")) mcool <- file.path(out_dir,"H1-hESC-HiC-4DNFI7JNCNFB.mcool") My_BrickContainer <- Create_many_Bricks_from_mcool( output_directory = out_dir, file_prefix = "Test", mcool = mcool, resolution = 50000, experiment_name = "A random 4DN dataset") Brick_load_data_from_mcool(Brick = My_BrickContainer, mcool = mcool, resolution = 50000, matrix_chunk = 2000, remove_prior = TRUE, norm_factor = "Iterative-Correction") ## End(Not run)
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