CreateBrick_from_mcool {HiCBricks} | R Documentation |
CreateBrick_from_mcool
is a wrapper on CreateBrick which creates the
Brick data structure from an mcool file.
CreateBrick_from_mcool(Brick, mcool, binsize = NULL, chrs = NULL, remove.existing = FALSE)
Brick |
Required. A string specifying the path to the Brick store created with CreateBrick. |
mcool |
Required. Path to an mcool file. |
binsize |
Optional. The binsize to select from an mcool file. |
chrs |
Optional. If provided will only create a Brick for these chromosomes (both cis & trans). |
remove.existing |
Optional. Default FALSE. If TRUE, will remove the HDF file with the same name and create a new one. By default, it will not replace existing files. |
mcool are a standard 4D nucleome data structure for Hi-C data. Read more about the 4D nucleome project here.
This function will generate the target Brick file. Upon completion, the function will provide the path to the created/tracked HDF file.
Brick_load_data_from_mcool
to load data from
the mcool to a Brick store.
## Not run: require(curl) curl_download(url = paste("https://data.4dnucleome.org/" "files-processed/4DNFI7JNCNFB/" "@download/4DNFI7JNCNFB.mcool",sep = ""), destfile = file.path(temp.dir(),"H1-hESC-HiC-4DNFI7JNCNFB.mcool")) Output.brick <- file.path(tempdir(), "H1-hESC-HiC-4DNFI7JNCNFB-10000-ICE-normalised-chr1.brick") mcool <- file.path(temp.dir(),"H1-hESC-HiC-4DNFI7JNCNFB.mcool") CreateBrick_from_mcool(Brick = Output.brick, mcool = mcool, binsize = 10000, chrs = "chr1") ## End(Not run)