HiContacts: R interface to cool files

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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