Contacts

This function has been deprecated in favor of the generic HiCExperiment() constructor (from HiCExperiment package).

Contacts(
  file,
  resolution = NULL,
  focus = NULL,
  metadata = list(),
  topologicalFeatures = S4Vectors::SimpleList(loops =
    S4Vectors::Pairs(GenomicRanges::GRanges(), GenomicRanges::GRanges()), borders =
    GenomicRanges::GRanges(), compartments = GenomicRanges::GRanges(), viewpoints =
    GenomicRanges::GRanges()),
  pairsFile = NULL
)

Arguments

file

Path to a (m)cool file

resolution

Resolution to use with mcool file

focus

focus Chr. coordinates for which interaction counts are extracted from the .(m)cool file, provided as a character string (e.g. "II:4001-5000"). If not provided, the entire (m)cool file will be imported.

metadata

list of metadata

topologicalFeatures

topologicalFeatures provided as a named SimpleList

pairsFile

Path to an associated .pairs file

Value

a new HiCExperiment object.

Examples

library(HiContacts)
library(HiContactsData)
#> Loading required package: ExperimentHub
#> Loading required package: BiocGenerics
#> 
#> Attaching package: ‘BiocGenerics’
#> The following object is masked from ‘package:HiCExperiment’:
#> 
#>     as.data.frame
#> The following objects are masked from ‘package:stats’:
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from ‘package:base’:
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#>     pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
#>     tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: AnnotationHub
#> Loading required package: BiocFileCache
#> Loading required package: dbplyr
mcool_path <- HiContactsData::HiContactsData('yeast_wt', 'mcool')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
Contacts(mcool_path, resolution = 1000)
#> Warning: `HiContacts::Contacts` is deprecated; see '?HiCExperiment::HiCExperiment' constructor instead.
#> `HiCExperiment` object with 8,757,906 contacts over 12,079 regions 
#> -------
#> fileName: "/github/home/.cache/R/ExperimentHub/1bea36c87b1b_7752" 
#> focus: "whole genome" 
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 1000 
#> interactions: 2945692 
#> scores(2): count balanced 
#> topologicalFeatures: loops(0) borders(0) compartments(0) viewpoints(0) 
#> pairsFile: N/A 
#> metadata(0):