# Analysing cool files in R with HiContacts

## Documentation for package ‘HiContacts’ version 1.13.0

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

## Help Pages

afmhotrColors | Matrix palettes
aggregate-method | HiContacts arithmetics functionalities
arithmetics | HiContacts arithmetics functionalities
autocorrelate | HiContacts arithmetics functionalities
bbrColors | Matrix palettes
bgrColors | Matrix palettes
boost | HiContacts arithmetics functionalities
bwrColors | Matrix palettes
cisTransRatio | cisTransRatio
coarsen | HiContacts arithmetics functionalities
Contacts | Contacts
coolerColors | Matrix palettes
coverage-method | Aligning tracks with HiCExperiment objects
despeckle | HiContacts arithmetics functionalities
detrend | HiContacts arithmetics functionalities
distanceLaw | Compute the law of distance-dependent contact frequency, a.k.a. P(s)
distanceLaw-method | Compute the law of distance-dependent contact frequency, a.k.a. P(s)
divide | HiContacts arithmetics functionalities
getBorders | Contact map insulation
getCompartments | Contact map compartments
getDiamondInsulation | Contact map insulation
getLoops | Finding loops in contact map
HiContacts-plots | HiContacts plotting functionalities
localDistanceLaw | Compute the law of distance-dependent contact frequency, a.k.a. P(s)
merge-method | HiContacts arithmetics functionalities
montage | Plotting a contact matrix
montage-method | Plotting a contact matrix
normalize-method | HiContacts arithmetics functionalities
palettes | Matrix palettes
plot4C | Plotting virtual 4C profiles
plotMatrix | Plotting a contact matrix
plotMatrix-method | Plotting a contact matrix
plotPs | Plotting a P(s) distance law
plotPsSlope | Plotting a P(s) distance law
plotSaddle | Plotting saddle plots
plotScalogram | Plotting scalograms
Ps | Compute the law of distance-dependent contact frequency, a.k.a. P(s)
rainbowColors | Matrix palettes
scalogram | Compute a scalogram of contacts
subsample | HiContacts arithmetics functionalities
tracks | Aligning tracks with HiCExperiment objects
virtual4C | Computing virtual 4C profiles