HiContacts: R interface to cool files


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Documentation for package ‘HiContacts’ version 1.0.0

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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