Package index

Importing Hi-C files

AllGenerics availableResolutions availableChromosomes resolutions resolution focus focus scores scores topologicalFeatures topologicalFeatures pairsFile pairsFile metadata bins slices zoom refocus cis trans bin

Generic functions

import() availableResolutions(<ANY>) availableResolutions(<CoolFile>) availableResolutions(<HicFile>) availableResolutions(<HicproFile>) availableChromosomes(<ANY>) availableChromosomes(<CoolFile>) availableChromosomes(<HicFile>) availableChromosomes(<HicproFile>)

HiCExperiment import methods

Exporting Hi-C files

export(<HiCExperiment>,<missing>,<character>)

HiCExperiment export methods

Methods for HiCExperiment S4 class

HiCExperiment() makeHiCExperimentFromGInteractions() resolutions(<HiCExperiment>) resolution(<HiCExperiment>) focus(<HiCExperiment>) `focus<-`(<HiCExperiment>,<character>) zoom(<HiCExperiment>,<numeric>) refocus(<HiCExperiment>,<character>) scores(<HiCExperiment>,<missing>) scores(<HiCExperiment>,<character>) scores(<HiCExperiment>,<numeric>) `scores<-`(<HiCExperiment>,<character>,<numeric>) topologicalFeatures(<HiCExperiment>,<missing>) topologicalFeatures(<HiCExperiment>,<character>) topologicalFeatures(<HiCExperiment>,<numeric>) `topologicalFeatures<-`(<HiCExperiment>,<character>,<GRangesOrGInteractions>) pairsFile(<HiCExperiment>) `pairsFile<-`(<HiCExperiment>,<character>) `metadata<-`(<HiCExperiment>,<list>) subsetByOverlaps(<HiCExperiment>,<numeric>) subsetByOverlaps(<HiCExperiment>,<logical>) subsetByOverlaps(<HiCExperiment>,<GRanges>) subsetByOverlaps(<HiCExperiment>,<GInteractions>) subsetByOverlaps(<HiCExperiment>,<Pairs>) `[`(<HiCExperiment>,<numeric>,<ANY>,<ANY>) `[`(<HiCExperiment>,<GRanges>,<ANY>,<ANY>) `[`(<HiCExperiment>,<logical>,<ANY>,<ANY>) `[`(<HiCExperiment>,<GInteractions>,<ANY>,<ANY>) `[`(<HiCExperiment>,<Pairs>,<ANY>,<ANY>) `[`(<HiCExperiment>,<character>,<ANY>,<ANY>) fileName(<HiCExperiment>) interactions(<HiCExperiment>) `interactions<-`(<HiCExperiment>,<GInteractions>) length(<HiCExperiment>) `$<-`(<HiCExperiment>) `$`(<HiCExperiment>) seqinfo(<HiCExperiment>) bins(<HiCExperiment>) anchors(<HiCExperiment>) regions(<HiCExperiment>) cis(<HiCExperiment>) trans(<HiCExperiment>)

HiCExperiment S4 class

AggrHiCExperiment() slices(<AggrHiCExperiment>,<missing>) slices(<AggrHiCExperiment>,<character>) slices(<AggrHiCExperiment>,<numeric>) show(<AggrHiCExperiment>)

AggrHiCExperiment S4 class

S4 Classes for Hi-C contact matrix file formats

ContactsFile-class ContactsFile ContactsFile-methods pairsFile,ContactsFile-method resolution,ContactsFile-method metadata metadata

ContactsFile S4 class

CoolFile-class McoolFile-class CoolFile CoolFile-methods show,CoolFile-method

CoolFile S4 class

HicFile-class HicFile HicFile-methods show,HicFile-method

HicFile S4 class

HicproFile-class HicproFile HicproFile-methods show,HicproFile-method

HicproFile S4 class

PairsFile-class PairsFile pairsFile,PairsFile-method

PairsFile S4 class

Coercing methods

bin(<GInteractions>,<numeric>) bin(<PairsFile>,<numeric>)

HiCExperiment binning methods

as.matrix(<HiCExperiment>) as.data.frame(<HiCExperiment>) gi2cm() cm2matrix() df2gi()

Coercing functions

Example datasets

centros_yeast contacts_yeast() contacts_yeast_eco1()

Example datasets provided in HiCExperiment & HiContactsData