High Throughput Chromosome Conformation Capture analysis

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Documentation for package ‘HiTC’ version 1.24.0

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A B C D E F G H I M N P R S X Y misc

-- A --

as.list-method Class 'HTClist'

-- B --

binningC Windowing of high-throughput 'C' contact matrix

-- C --

c-method Class 'HTCexp'
c-method Class 'HTClist'
CQC Quality Control for high-throughput 'C' experiment

-- D --

detail Class 'HTCexp'
detail-method Class 'HTCexp'
detail-method Class 'HTClist'
detail-methods Class 'HTCexp'
directionalityIndex Directionality index calculation
discretize Transform matrix of counts data into discrete matrix
divide Class 'HTCexp'
divide-method Class 'HTCexp'
divide-methods Class 'HTCexp'

-- E --

E14 HiTC - 5C data
export-defunct Class 'HTCexp'
export.my5C Export 'HTCexp' object to my5C website format
exportC Export 'HTCexp' object
extractRegion Extract a subset of the HTCexp object

-- F --

forcePairwise Class 'HTClist'
forcePairwise-method Class 'HTClist'
forceSymmetric-method Class 'HTCexp'
forceSymmetric-method Class 'HTClist'
forceTriangular Class 'HTCexp'
forceTriangular-method Class 'HTCexp'

-- G --

getAnnotatedRestrictionSites Annotation of restriction sites
getCombinedContacts Class 'HTClist'
getCombinedContacts-method Class 'HTClist'
getCombinedIntervals Class 'HTClist'
getCombinedIntervals-method Class 'HTClist'
getExpectedCounts Estimate expected interaction counts of a High-Throughput C intrachromsomal map based on the genomic distance between two loci
getPearsonMap Pearson correlation map
getRestrictionFragmentsPerChromosome Get a list of DNA restriction fragments

-- H --

HTCexp Class 'HTCexp'
HTCexp-class Class 'HTCexp'
HTClist Class 'HTClist'
HTClist-class Class 'HTClist'

-- I --

id Class 'HTCexp'
id-method Class 'HTCexp'
id-methods Class 'HTCexp'
import.my5C Import data from my5C webtool
importC Import high-htroughput 'C' data
intdata Class 'HTCexp'
intdata-method Class 'HTCexp'
intdata<- Class 'HTCexp'
intdata<--method Class 'HTCexp'
intdata<--methods Class 'HTCexp'
intervalsDist intervalsDist
isBinned Class 'HTCexp'
isBinned-method Class 'HTCexp'
isBinned-method Class 'HTClist'
isBinned-methods Class 'HTCexp'
isComplete Class 'HTClist'
isComplete-method Class 'HTClist'
isComplete-methods Class 'HTClist'
isIntraChrom Class 'HTCexp'
isIntraChrom-method Class 'HTCexp'
isIntraChrom-method Class 'HTClist'
isIntraChrom-methods Class 'HTCexp'
isPairwise Class 'HTClist'
isPairwise-method Class 'HTClist'
isSymmetric Class 'HTCexp'
isSymmetric-method Class 'HTCexp'
isSymmetric-methods Class 'HTCexp'
isTriangular-method Class 'HTCexp'
isTriangular-methods Class 'HTCexp'

-- M --

mapC Visualize 'C' ontact map
mapC-method Visualize 'C' ontact map
mapC-methods Visualize 'C' ontact map
MEF HiTC - 5C data

-- N --

Nora_5C HiTC - 5C data
normICE Iterative Correction of Hi-C data (ICE)
normLGF Local Genomic Feature (LGF) normalization
normPerExpected Class 'HTCexp'
normPerExpected-method Class 'HTCexp'
normPerExpected-method Class 'HTClist'
normPerExpected-methods Class 'HTCexp'
normPerReads Class 'HTCexp'
normPerReads-method Class 'HTCexp'
normPerReads-methods Class 'HTCexp'
normPerTrans Class 'HTCexp'
normPerTrans-method Class 'HTCexp'
normPerTrans-methods Class 'HTCexp'
normPerZscore-defunct Class 'HTCexp'

-- P --

pca.hic Perform Principle Component Analysis on Hi-C contact map
plot-method Class 'HTCexp'
plot-method Class 'HTClist'

-- R --

range Class 'HTCexp'
range-method Class 'HTCexp'
range-method Class 'HTClist'
ranges Class 'HTClist'
ranges-method Class 'HTClist'
ranges-methods Class 'HTClist'
reduce Class 'HTClist'
reduce-method Class 'HTClist'
reduce-methods Class 'HTClist'
removeIntervals Remove intervals from HTCexp object

-- S --

seqlevels Class 'HTCexp'
seqlevels-method Class 'HTCexp'
seqlevels-method Class 'HTClist'
seq_name-deprecated Class 'HTCexp'
setGenomicFeatures Annotation of Hi-C contact map
setIntervalScale Set x and y interval of the HTCexp object
show-method Class 'HTCexp'
show-method Class 'HTClist'
substract Class 'HTCexp'
substract-method Class 'HTCexp'
substract-methods Class 'HTCexp'
summary-method Class 'HTCexp'
summary-method Class 'HTClist'

-- X --

xy_intervals Class 'HTCexp'
xy_intervals-method Class 'HTCexp'
xy_intervals-methods Class 'HTCexp'
x_intervals Class 'HTCexp'
x_intervals-method Class 'HTCexp'
x_intervals-methods Class 'HTCexp'
x_intervals<- Class 'HTCexp'
x_intervals<--method Class 'HTCexp'
x_intervals<--methods Class 'HTCexp'

-- Y --

y_intervals Class 'HTCexp'
y_intervals-method Class 'HTCexp'
y_intervals-methods Class 'HTCexp'
y_intervals<- Class 'HTCexp'
y_intervals<--method Class 'HTCexp'
y_intervals<--methods Class 'HTCexp'

-- misc --

[-method Class 'HTClist'