# HiContacts: R interface to cool files

## Documentation for package ‘HiContacts’ version 1.0.0

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

## Help Pages

A B C D F G H I L M P R S T V misc

## -- A --

afmhotrColors | Matrix palettes
anchors | 'Contacts' S4 class and methods
anchors-method | 'Contacts' S4 class and methods
are_contacts | Checks functions
asGInteractions | Utils functions
autocorrelate | Arithmetics with (m)cool file(s)

## -- B --

bbrColors | Matrix palettes
bins | 'Contacts' S4 class and methods
bins-method | 'Contacts' S4 class and methods
bwrColors | Matrix palettes

## -- C --

centros_yeast | Example datasets provided in 'HiContacts' & 'HiContactsData'
char2coords | Utils functions
check_cool_file | Checks functions
check_cool_format | Checks functions
check_resolution | Checks functions
cisTransRatio | cisTransRatio
cm2matrix | Parsing (m)cool files
Contacts | 'Contacts' S4 class and methods
Contacts-class | 'Contacts' S4 class and methods
contacts_yeast | Example datasets provided in 'HiContacts' & 'HiContactsData'
contacts_yeast_eco1 | Example datasets provided in 'HiContacts' & 'HiContactsData'
cool2gi | Parsing (m)cool files
cool2seqinfo | Parsing (m)cool files
coords2char | Utils functions

## -- D --

detrend | Arithmetics with (m)cool file(s)
distanceLaw | Compute the law of distance-dependent contact frequency, a.k.a. P(s)
divide | Arithmetics with (m)cool file(s)

## -- F --

fetchCool | Parsing (m)cool files
fileName | 'Contacts' S4 class and methods
fileName-method | 'Contacts' S4 class and methods
focus | 'Contacts' S4 class and methods
focus-method | 'Contacts' S4 class and methods
focus<- | 'Contacts' S4 class and methods
focus<--method | 'Contacts' S4 class and methods
fullContactInteractions | Utils functions
full_contacts_yeast | Example datasets provided in 'HiContacts' & 'HiContactsData'

## -- G --

getAnchors | Parsing (m)cool files
getCounts | Parsing (m)cool files
getCountsFromPair | Parsing (m)cool files
getHicStats | Utils functions
ggMatrix | Plotting a contact matrix
ggthemeHiContacts | ggplot2-related functions
gi2cm | Parsing (m)cool files

## -- H --

HiContacts package | HiContacts package

## -- I --

interactions | 'Contacts' S4 class and methods
interactions-method | 'Contacts' S4 class and methods
interactions<- | 'Contacts' S4 class and methods
interactions<--method | 'Contacts' S4 class and methods
is_comparable | Checks functions
is_cool | Checks functions
is_mcool | Checks functions
is_same_bins | Checks functions
is_same_regions | Checks functions
is_same_resolution | Checks functions
is_same_seqinfo | Checks functions
is_square | Checks functions
is_symmetrical | Checks functions

## -- L --

length | 'Contacts' S4 class and methods
length-method | 'Contacts' S4 class and methods
localDistanceLaw | Compute the law of distance-dependent contact frequency, a.k.a. P(s)
lsCoolFiles | Parsing (m)cool files
lsCoolResolutions | Parsing (m)cool files

## -- M --

merge | Arithmetics with (m)cool file(s)
metadata<- | 'Contacts' S4 class and methods
metadata<--method | 'Contacts' S4 class and methods

## -- P --

pairs2gi | Parsing (m)cool files
pairsFile | 'Contacts' S4 class and methods
pairsFile-method | 'Contacts' S4 class and methods
pairsFile<- | 'Contacts' S4 class and methods
pairsFile<--method | 'Contacts' S4 class and methods
peekCool | Parsing (m)cool files
plot4C | Plotting virtual 4C profiles
plotMatrix | Plotting a contact matrix
plotPs | Plotting a P(s) distance law
plotPsSlope | Plotting a P(s) distance law
PsBreaks | Compute the law of distance-dependent contact frequency, a.k.a. P(s)

## -- R --

regions | 'Contacts' S4 class and methods
regions-method | 'Contacts' S4 class and methods
resolution | 'Contacts' S4 class and methods
resolution-method | 'Contacts' S4 class and methods
resolutions | 'Contacts' S4 class and methods
resolutions-method | 'Contacts' S4 class and methods

## -- S --

scores | 'Contacts' S4 class and methods
scores-method | 'Contacts' S4 class and methods
scores<- | 'Contacts' S4 class and methods
scores<--method | 'Contacts' S4 class and methods
sdiag<- | Utils functions
seqinfo-method | 'Contacts' S4 class and methods
serpentinify | Arithmetics with (m)cool file(s)
setAs | 'Contacts' S4 class and methods
setAs-method | 'Contacts' S4 class and methods
show | 'Contacts' S4 class and methods
show-method | 'Contacts' S4 class and methods
sortPairs | Utils functions
splitCoords | Utils functions
summary | 'Contacts' S4 class and methods
summary-method | 'Contacts' S4 class and methods

## -- T --

topologicalFeatures | 'Contacts' S4 class and methods
topologicalFeatures-method | 'Contacts' S4 class and methods
topologicalFeatures<- | 'Contacts' S4 class and methods
topologicalFeatures<--method | 'Contacts' S4 class and methods

## -- V --

virtual4C | Computing virtual 4C profiles

## -- misc --

[ | 'Contacts' S4 class and methods
[-method | 'Contacts' S4 class and methods