Brick_load_data_from_mcool {HiCBricks} | R Documentation |
Read an mcool contact matrix coming out of 4D nucleome projects into a Brick store.
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")
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. |
Returns TRUE if all went well.
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.
## 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)