ContactsFile S4 class

The ContactsFile class describes a BiocFile object, pointing to the location of an Hi-C matrix file (cool, mcool, hic, hicpro, ...) and containing additional slots:

1. resolution: at which resolution the associated mcool 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. If the CoolFile is created by HiCool, it will contain two elements: log (path to HiCool processing log file) and stats (aggregating some stats from HiCool mapping).

ContactsFile methods.

Arguments

path

String; path to an Hi-C matrix file (cool, mcool, hic, hicpro)

resolution

numeric; resolution to use with Hi-C matrix file

pairsFile

String; path to a pairs file

metadata

list.

object

A ContactsFile object.

x

A ContactsFile object.

Slots

resolution

numeric value or NULL

pairsFile

PairsFile object

metadata

list

See also

CoolFile(), HicFile(), HicproFile()