# High Throughput Chromosome Conformation Capture analysis

## Documentation for package ‘HiTC’ version 1.20.0

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

## Help Pages

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'