CQC                     Quality Control for high-throughput 'C'
                        experiment
HTCexp-class            Class 'HTCexp'
HTClist-class           Class 'HTClist'
Nora_5C                 HiTC - 5C data
binningC                Windowing of high-throughput 'C' contact matrix
directionalityIndex     Directionality index calculation
discretize              Transform matrix of counts data into discrete
                        matrix
export.my5C             Export 'HTCexp' object to my5C website format
exportC                 Export 'HTCexp' object
extractRegion           Extract a subset of the HTCexp object
getAnnotatedRestrictionSites
                        Annotation of restriction sites
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
import.my5C             Import data from my5C webtool
importC                 Import high-htroughput 'C' data
intervalsDist           intervalsDist
mapC                    Visualize 'C' ontact map
normICE                 Iterative Correction of Hi-C data (ICE)
normLGF                 Local Genomic Feature (LGF) normalization
pca.hic                 Perform Principle Component Analysis on Hi-C
                        contact map
removeIntervals         Remove intervals from HTCexp object
setGenomicFeatures      Annotation of Hi-C contact map
setIntervalScale        Set x and y interval of the HTCexp object
