| Title: | 4DN data package |
|---|---|
| Description: | fourDNData is a data package giving programmatic access to Hi-C contact matrices uniformly processed by the [4DN consortium](https://www.4dnucleome.org/). The matrices are available in the multi-resolution `.mcool` format. |
| Authors: | Jacques Serizay [aut, cre] |
| Maintainer: | Jacques Serizay <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.12.0 |
| Built: | 2026-10-10 11:17:03 UTC |
| Source: | https://github.com/bioc/fourDNData |
Fetches files from the 4DN data portal and caches them using the BiocFileCache system.
experimentSetAccession |
Any 4DN-provided experimentSet Accession number (check https://data.4dnucleome.org/browse/) for a browser-based explorer. |
type |
any of c('pairs', 'hic', 'mcool', 'boundaries', 'insulation', 'compartments') |
.fetch_pairs |
Whether to also download the associated pairs file |
fourDNData() returns the local path of the queried file
cached with BiocFileCache. fourDNHiCExperiment() returns a
HiCExperiment object with populated metadata and topologicalFeatures (
if available).
#################################### ## Importing individual 4DN files ## #################################### head(fourDNData()) mcf <- fourDNData(experimentSetAccession = '4DNESDP9ECMN', type = 'mcool') mcf #################################### ## Importing full 4DN experiments ## #################################### id <- fourDNData() |> dplyr::filter( experimentType == 'in situ Hi-C', biosource == 'GM12878', publication == 'Sanborn AL et al. (2015)' ) |> dplyr::arrange(size) |> dplyr::pull(experimentSetAccession) |> unique() id[1] x <- fourDNHiCExperiment(id[1]) x HiCExperiment::topologicalFeatures(x) S4Vectors::metadata(x)$`4DN_info`#################################### ## Importing individual 4DN files ## #################################### head(fourDNData()) mcf <- fourDNData(experimentSetAccession = '4DNESDP9ECMN', type = 'mcool') mcf #################################### ## Importing full 4DN experiments ## #################################### id <- fourDNData() |> dplyr::filter( experimentType == 'in situ Hi-C', biosource == 'GM12878', publication == 'Sanborn AL et al. (2015)' ) |> dplyr::arrange(size) |> dplyr::pull(experimentSetAccession) |> unique() id[1] x <- fourDNHiCExperiment(id[1]) x HiCExperiment::topologicalFeatures(x) S4Vectors::metadata(x)$`4DN_info`
Managing 4DN data downloads via the integrated
BiocFileCache system.
fourDNDataCache(...)fourDNDataCache(...)
... |
Arguments passed to internal |
BiocFileCache object
bfc <- fourDNDataCache() bfc BiocFileCache::bfcinfo(bfc)bfc <- fourDNDataCache() bfc BiocFileCache::bfcinfo(bfc)