# Bioconductor class for interacting with Hi-C files in R

## Documentation for package ‘HiCExperiment’ version 1.11.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

$-method | 'HiCExperiment' S4 class
$<--method | 'HiCExperiment' S4 class
AggrHiCExperiment | 'AggrHiCExperiment' S4 class
AggrHiCExperiment-class | 'AggrHiCExperiment' S4 class
anchors-method | 'HiCExperiment' S4 class
as | Coercing functions
as.data.frame-method | Coercing functions
as.matrix-method | Coercing functions
availableChromosomes-method | HiCExperiment import methods
availableResolutions-method | HiCExperiment import methods
bin-method | HiCExperiment binning methods
bin-methods | HiCExperiment binning methods
bins-method | 'HiCExperiment' S4 class
centros_yeast | Example datasets provided in 'HiCExperiment' & 'HiContactsData'
cis-method | 'HiCExperiment' S4 class
cm2matrix | Coercing functions
coerce-method | Coercing functions
ContactsFile | 'ContactsFile' S4 class
ContactsFile-class | 'ContactsFile' S4 class
ContactsFile-methods | 'ContactsFile' S4 class
contacts_yeast | Example datasets provided in 'HiCExperiment' & 'HiContactsData'
contacts_yeast_eco1 | Example datasets provided in 'HiCExperiment' & 'HiContactsData'
CoolFile | 'CoolFile' S4 class
CoolFile-class | 'CoolFile' S4 class
CoolFile-methods | 'CoolFile' S4 class
data | Example datasets provided in 'HiCExperiment' & 'HiContactsData'
df2gi | Coercing functions
export | HiCExperiment export methods
export-method | HiCExperiment export methods
export-methods | HiCExperiment export methods
fileName-method | 'HiCExperiment' S4 class
focus-method | 'HiCExperiment' S4 class
focus<--method | 'HiCExperiment' S4 class
gi2cm | Coercing functions
HiCExperiment | 'HiCExperiment' S4 class
HiCExperiment-class | 'HiCExperiment' S4 class
HicFile | 'HicFile' S4 class
HicFile-class | 'HicFile' S4 class
HicFile-methods | 'HicFile' S4 class
HicproFile | 'HicproFile' S4 class
HicproFile-class | 'HicproFile' S4 class
HicproFile-methods | 'HicproFile' S4 class
import | HiCExperiment import methods
import-method | HiCExperiment import methods
import-methods | HiCExperiment import methods
interactions-method | 'HiCExperiment' S4 class
interactions<--method | 'HiCExperiment' S4 class
length-method | 'HiCExperiment' S4 class
makeHiCExperimentFromGInteractions | 'HiCExperiment' S4 class
McoolFile-class | 'CoolFile' S4 class
metadata<--method | 'ContactsFile' S4 class
metadata<--method | 'HiCExperiment' S4 class
PairsFile | 'PairsFile' S4 class
PairsFile-class | 'PairsFile' S4 class
pairsFile-method | 'ContactsFile' S4 class
pairsFile-method | 'HiCExperiment' S4 class
pairsFile-method | 'PairsFile' S4 class
pairsFile<--method | 'HiCExperiment' S4 class
refocus-method | 'HiCExperiment' S4 class
regions-method | 'HiCExperiment' S4 class
resolution-method | 'ContactsFile' S4 class
resolution-method | 'HiCExperiment' S4 class
resolutions-method | 'HiCExperiment' S4 class
scores-method | 'HiCExperiment' S4 class
scores<--method | 'HiCExperiment' S4 class
seqinfo-method | 'HiCExperiment' S4 class
show-method | 'AggrHiCExperiment' S4 class
show-method | 'CoolFile' S4 class
show-method | 'HiCExperiment' S4 class
show-method | 'HicFile' S4 class
show-method | 'HicproFile' S4 class
slices-method | 'AggrHiCExperiment' S4 class
subsetByOverlaps-method | 'HiCExperiment' S4 class
topologicalFeatures-method | 'HiCExperiment' S4 class
topologicalFeatures<--method | 'HiCExperiment' S4 class
trans-method | 'HiCExperiment' S4 class
zoom-method | 'HiCExperiment' S4 class
[-method | 'HiCExperiment' S4 class