Package: HiCExperiment 1.5.0

Jacques Serizay

HiCExperiment: Bioconductor class for interacting with Hi-C files in R

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.

Authors:Jacques Serizay [aut, cre]

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HiCExperiment.pdf |HiCExperiment.html✨
HiCExperiment/json (API)

# Install 'HiCExperiment' in R:

install.packages('HiCExperiment', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/js2264/hicexperiment/issues

Datasets:

centros_yeast - Example datasets provided in 'HiCExperiment' & 'HiContactsData'

On BioConductor:HiCExperiment-1.5.0(bioc 3.20)HiCExperiment-1.4.0(bioc 3.19)

bioconductor-package

45 exports 1.24 score 66 dependencies 2 dependents

Last updated 2 months agofrom:6d012594e0

Exports:AggrHiCExperiment anchors as as.data.frame as.matrix availableChromosomes availableResolutions bins cis cm2matrix contacts_yeast contacts_yeast_eco1 CoolFile df2gi export fileName focus focus<-gi2cm HiCExperiment HicFile HicproFile import interactions interactions<-makeHiCExperimentFromGInteractions metadata metadata<-pairsFile PairsFile pairsFile<-refocus regions resolution resolutions scores scores<-seqinfo show slices subsetByOverlaps topologicalFeatures topologicalFeatures<-trans zoom

Dependencies:abind askpass BH Biobase BiocGenerics BiocIO BiocParallel bit bit64 cli codetools cpp11 crayon curl DelayedArray dplyr fansi formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue hms httr InteractionSet IRanges jsonlite lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig prettyunits progress R6 Rcpp rhdf5 rhdf5filters Rhdf5lib rlang S4Arrays S4Vectors snow SparseArray strawr SummarizedExperiment sys tibble tidyselect tzdb UCSC.utils utf8 vctrs vroom withr XVector zlibbioc

Introduction to HiCExperiment

Jacques Serizay

Rendered fromHiCExperiment.Rmdusingknitr::rmarkdownon Jun 21 2024.

Last update: 2024-01-10
Started: 2022-11-17

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
'AggrHiCExperiment' S4 class	AggrHiCExperiment AggrHiCExperiment-class show,AggrHiCExperiment-method slices,AggrHiCExperiment,character-method slices,AggrHiCExperiment,missing-method slices,AggrHiCExperiment,numeric-method
Coercing functions	as as.data.frame,HiCExperiment-method as.matrix,HiCExperiment-method cm2matrix coerce,HiCExperiment,ContactMatrix-method coerce,HiCExperiment,data.frame-method coerce,HiCExperiment,GInteractions-method coerce,HiCExperiment,InteractionSet-method coerce,HiCExperiment,matrix-method df2gi gi2cm
HiCExperiment binning methods	bin,GInteractions,character-method bin,GInteractions,numeric-method bin,PairsFile,numeric-method bin-methods
'ContactsFile' S4 class	ContactsFile ContactsFile-class ContactsFile-methods metadata<-,ContactsFile,list-method metadata<-,ContactsFile-method pairsFile,ContactsFile-method resolution,ContactsFile-method
'CoolFile' S4 class	CoolFile CoolFile-class CoolFile-methods McoolFile-class show,CoolFile-method
Example datasets provided in 'HiCExperiment' & 'HiContactsData'	centros_yeast contacts_yeast contacts_yeast_eco1 data
HiCExperiment export methods	export export,HiCExperiment,missing,character-method export-methods
'HiCExperiment' S4 class	$,HiCExperiment-method $<-,HiCExperiment-method anchors,HiCExperiment-method bins,HiCExperiment-method cis,HiCExperiment-method fileName,HiCExperiment-method focus,HiCExperiment-method focus<-,HiCExperiment,character-method focus<-,HiCExperiment-method HiCExperiment HiCExperiment-class interactions,HiCExperiment-method interactions<-,HiCExperiment,GInteractions-method interactions<-,HiCExperiment-method length,HiCExperiment-method makeHiCExperimentFromGInteractions metadata<-,HiCExperiment,list-method metadata<-,HiCExperiment-method pairsFile,HiCExperiment-method pairsFile<-,HiCExperiment,character-method pairsFile<-,HiCExperiment-method refocus,HiCExperiment,character-method regions,HiCExperiment-method resolution,HiCExperiment-method resolutions,HiCExperiment-method scores,HiCExperiment,character-method scores,HiCExperiment,missing-method scores,HiCExperiment,numeric-method scores,HiCExperiment-method scores<-,HiCExperiment,character,numeric-method scores<-,HiCExperiment-method seqinfo,HiCExperiment-method show,HiCExperiment-method subsetByOverlaps,HiCExperiment,GInteractions-method subsetByOverlaps,HiCExperiment,GRanges-method subsetByOverlaps,HiCExperiment,logical-method subsetByOverlaps,HiCExperiment,numeric-method subsetByOverlaps,HiCExperiment,Pairs-method topologicalFeatures,HiCExperiment,character-method topologicalFeatures,HiCExperiment,missing-method topologicalFeatures,HiCExperiment,numeric-method topologicalFeatures,HiCExperiment-method topologicalFeatures<-,HiCExperiment,character,GRangesOrGInteractions-method topologicalFeatures<-,HiCExperiment-method trans,HiCExperiment-method zoom,HiCExperiment,numeric-method [,HiCExperiment,character,ANY,ANY-method [,HiCExperiment,GInteractions,ANY,ANY-method [,HiCExperiment,GRanges,ANY,ANY-method [,HiCExperiment,logical,ANY,ANY-method [,HiCExperiment,numeric,ANY,ANY-method [,HiCExperiment,Pairs,ANY,ANY-method [,HiCExperiment-method
'HicFile' S4 class	HicFile HicFile-class HicFile-methods show,HicFile-method
'HicproFile' S4 class	HicproFile HicproFile-class HicproFile-methods show,HicproFile-method
HiCExperiment import methods	availableChromosomes,ANY-method availableChromosomes,CoolFile-method availableChromosomes,HicFile-method availableChromosomes,HicproFile-method availableResolutions,ANY-method availableResolutions,CoolFile-method availableResolutions,HicFile-method availableResolutions,HicproFile-method import import,CoolFile,ANY,ANY-method import,CoolFile-method import,HicFile,ANY,ANY-method import,HicFile-method import,HicproFile,ANY,ANY-method import,HicproFile-method import,PairsFile,ANY,ANY-method import,PairsFile-method import-methods
'PairsFile' S4 class	PairsFile pairsFile,PairsFile-method PairsFile-class