Import methods to parse Hi-C files (.(m)cool, .hic, HiC-Pro derived
matrices, pairs files) into data structures implemented in the
HiCExperiment package.
Usage
import(con, format, text, ...)
# S4 method for class 'ANY'
availableResolutions(x, ...)
# S4 method for class 'CoolFile'
availableResolutions(x)
# S4 method for class 'HicFile'
availableResolutions(x)
# S4 method for class 'HicproFile'
availableResolutions(x)
# S4 method for class 'ANY'
availableChromosomes(x, ...)
# S4 method for class 'CoolFile'
availableChromosomes(x)
# S4 method for class 'HicFile'
availableChromosomes(x)
# S4 method for class 'HicproFile'
availableChromosomes(x)Arguments
- ...
Extra parameters to pass to format-specific methods. A list of possible arguments is provided in the next section.
- con, x
Path or connection to a cool, mcool, .hic or HiC-Pro derived files. Can also be a path to a pairs file.
- format
The format of the output. If missing and 'con' is a filename, the format is derived from the file extension. This argument is unnecessary when files are directly provided as
CoolFile,HicFile,HicproFileorPairsFile.- text
If 'con' is missing, this can be a character vector directly providing the string data to import.
import arguments for ContactFile class
ContactFile class gathers CoolFile, HicFile and HicproFile classes.
When importing a ContactFile object in R, two main arguments can be
provided besides the ContactFile itself:
resolution: Resolutions available in the disk-stored contact matrix can be listed usingavailableResolutions(file)focus: A genomic locus (or pair of loci) provided as a string. It can be any of the following string structures:"II"or"II:20001-30000": this will extract a symmetrical square HiCExperiment object, of an entire chromosome or an portion of it."II|III"or"II:20001-30000|III:40001-90000": this will extract a non-symmetrical HiCExperiment object, with an entire or portion of different chromosomes on each axis.
Examples
################################################################
## ----------- Importing .(m)cool contact matrices ---------- ##
################################################################
mcoolPath <- HiContactsData::HiContactsData('yeast_wt', 'mcool')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
availableResolutions(mcoolPath)
#> resolutions(5): 1000 2000 4000 8000 16000
#>
availableChromosomes(mcoolPath)
#> Seqinfo object with 16 sequences from an unspecified genome:
#> seqnames seqlengths isCircular genome
#> I 230218 <NA> <NA>
#> II 813184 <NA> <NA>
#> III 316620 <NA> <NA>
#> IV 1531933 <NA> <NA>
#> V 576874 <NA> <NA>
#> ... ... ... ...
#> XII 1078177 <NA> <NA>
#> XIII 924431 <NA> <NA>
#> XIV 784333 <NA> <NA>
#> XV 1091291 <NA> <NA>
#> XVI 948066 <NA> <NA>
import(mcoolPath, resolution = 16000, focus = 'XVI', format = 'cool')
#> `HiCExperiment` object with 535,350 contacts over 60 regions
#> -------
#> fileName: "/github/home/.cache/R/ExperimentHub/190530f4def5_7752"
#> focus: "XVI"
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 16000
#> interactions: 1731
#> scores(2): count balanced
#> topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0)
#> pairsFile: N/A
#> metadata(0):
################################################################
## ------------ Importing .hic contact matrices ------------- ##
################################################################
hicPath <- HiContactsData::HiContactsData('yeast_wt', 'hic')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
availableResolutions(hicPath)
#> resolutions(5): 1000 2000 4000 8000 16000
#>
availableChromosomes(hicPath)
#> Seqinfo object with 17 sequences from an unspecified genome:
#> seqnames seqlengths isCircular genome
#> I 230218 <NA> <NA>
#> II 813184 <NA> <NA>
#> III 316620 <NA> <NA>
#> IV 1531933 <NA> <NA>
#> IX 439888 <NA> <NA>
#> ... ... ... ...
#> XIII 924431 <NA> <NA>
#> XIV 784333 <NA> <NA>
#> XV 1091291 <NA> <NA>
#> XVI 948066 <NA> <NA>
#> M 85780 <NA> <NA>
import(hicPath, resolution = 16000, focus = 'XVI', format = 'hic')
#> `HiCExperiment` object with 838,222 contacts over 60 regions
#> -------
#> fileName: "/github/home/.cache/R/ExperimentHub/19051c0d78f1_7836"
#> focus: "XVI"
#> resolutions(5): 1000 2000 4000 8000 16000
#> active resolution: 16000
#> interactions: 1732
#> scores(2): count balanced
#> topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0)
#> pairsFile: N/A
#> metadata(0):
################################################################
## ------- Importing HiC-Pro derived contact matrices ------- ##
################################################################
hicproMatrixPath <- HiContactsData::HiContactsData('yeast_wt', 'hicpro_matrix')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
hicproBedPath <- HiContactsData::HiContactsData('yeast_wt', 'hicpro_bed')
#> see ?HiContactsData and browseVignettes('HiContactsData') for documentation
#> loading from cache
availableResolutions(hicproMatrixPath, hicproBedPath)
#> [1] 1000
availableChromosomes(hicproMatrixPath, hicproBedPath)
#> Seqinfo object with 17 sequences from an unspecified genome:
#> seqnames seqlengths isCircular genome
#> I 230218 <NA> <NA>
#> II 813184 <NA> <NA>
#> III 316620 <NA> <NA>
#> IV 1531933 <NA> <NA>
#> IX 439888 <NA> <NA>
#> ... ... ... ...
#> XII 1078177 <NA> <NA>
#> XIII 924431 <NA> <NA>
#> XIV 784333 <NA> <NA>
#> XV 1091291 <NA> <NA>
#> XVI 948066 <NA> <NA>
import(hicproMatrixPath, bed = hicproBedPath, format = 'hicpro')
#> Registered S3 methods overwritten by 'readr':
#> method from
#> as.data.frame.spec_tbl_df vroom
#> as_tibble.spec_tbl_df vroom
#> format.col_spec vroom
#> print.col_spec vroom
#> print.collector vroom
#> print.date_names vroom
#> print.locale vroom
#> str.col_spec vroom
#>
#> `HiCExperiment` object with 9,503,604 contacts over 12,165 regions
#> -------
#> fileName: "/github/home/.cache/R/ExperimentHub/19054ee69513_7837"
#> focus: "whole genome"
#> resolutions(1): 1000
#> active resolution: 1000
#> interactions: 2686250
#> scores(2): count balanced
#> topologicalFeatures: compartments(0) borders(0) loops(0) viewpoints(0)
#> pairsFile: N/A
#> metadata(1): regions