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HicFile S4 class

Source: R/HicFile-class.R, R/HicFile-methods.R
HicFile-class.Rd

The HicFile class describes a BiocFile object, pointing to the location of a .hic file (usually created with juicer) and containing 3 additional slots:

  1. resolution: at which resolution the associated .hic file should be parsed;

  2. pairsFile: the path (in plain character) to an optional pairs file (stored as a PairsFile object);

  3. metadata: a list metadata

HicFile methods.

Arguments

path

String; path to a .hic file

resolution

numeric; resolution to use with mcool file

pairsFile

String; path to a pairs file

metadata

list.

object

A HicFile object.

See also

CoolFile(), HicproFile()

Examples

hicPath <- HiContactsData::HiContactsData('yeast_wt', 'hic')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
pairsPath <- HiContactsData::HiContactsData('yeast_wt', 'pairs.gz')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
hic <- HicFile(
  hicPath, 
  resolution = 16000, 
  pairsFile = pairsPath, 
  metadata = list(type = 'example')
)
hic
#> HicFile object
#> .hic file: /github/home/.cache/R/ExperimentHub/19051c0d78f1_7836 
#> resolution: 16000 
#> pairs file: /github/home/.cache/R/ExperimentHub/190524de862e_7753 
#> metadata(1): type
resolution(hic)
#> [1] 16000
pairsFile(hic)
#>                                                  EH7703 
#> "/github/home/.cache/R/ExperimentHub/190524de862e_7753" 
metadata(hic)
#> $type
#> [1] "example"
#>