R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be further investigated in R using the `HiContacts` analysis package.
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library(HiCExperiment)
library(HiContactsData)
# Retrieve a sample cool file path
cool_file <- HiContactsData('yeast_wt', format = 'cool')
# Import the contact matrix as a HiCExperiment object
hic <- import(cool_file, format = 'cool', focus = 'I:20001-80000')
# Inspect the imported object
resolution(hic)
Input: A path to a .cool, .mcool, .hic, or HiC-Pro contact matrix file.
Output: A parsed HiCExperiment object containing contact frequencies, genomic bins, and metadata.
.cool, .mcool, .hic, or HiC-Pro formats using import().focus argument.GInteractions, ContactMatrix, or base matrix using as().HiContacts instead of HiCExperiment alone.HiCExperiment does not support the focus argument for HiC-Pro files (they must be fully imported into memory)..cool, .mcool, .hic, or HiC-Pro format (which consists of a .matrix and a .bed file)..pairs or .pairs.gz files can be linked using CoolFile(), HicFile(), or HicproFile() via the pairsFile argument.'cool', 'pairs').'I:20001-80000' or 'II:1-500000|II:100001-300000') to subset contacts within a genomic locus of interest.availableResolutions() before importing.availableChromosomes() to construct valid focus queries.bins() or unique regions using regions().focus: This is unsupported and will cause the entire matrix to be imported into memory.scores(hic) first.InteractionSet: For general representation of genomic interactions without specialized Hi-C file parsers.还没有评价。欢迎分享你的使用感受。
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