All functions

Contacts()

Contacts

HiContacts-plots

HiContacts plotting functionalities

distanceLaw() localDistanceLaw()

Compute the law of distance-dependent contact frequency, a.k.a. P(s)

aggregate(<HiCExperiment>) detrend() autocorrelate() divide() merge(<HiCExperiment>,<HiCExperiment>) despeckle() boost() coarsen() normalize(<HiCExperiment>) subsample()

HiContacts arithmetics functionalities

cisTransRatio()

cisTransRatio

getCompartments()

Contact map compartments

getDiamondInsulation() getBorders()

Contact map insulation

getLoops()

Finding loops in contact map

bwrColors() bbrColors() bgrColors() afmhotrColors() coolerColors() rainbowColors()

Matrix palettes

plot4C()

Plotting virtual 4C profiles

plotMatrix() montage()

Plotting a contact matrix

plotPs() plotPsSlope()

Plotting a P(s) distance law

plotSaddle()

Plotting saddle plots

plotScalogram()

Plotting scalograms

scalogram()

Compute a scalogram of contacts

coverage(<HiCExperiment>)

Aligning tracks with HiCExperiment objects

virtual4C()

Computing virtual 4C profiles