addCor                  Add correlation of ChIP-seq coverage to motif
                        pairs.
addCovCor               Add correlation of anchor signals to pairs of
                        close genomic regions.
addCovToGR              Add coverage to regions in 'GRanges' object.
addInteractionSupport   Add column to 'GInteractions' with overlap
                        support.
addMotifScore           Add motif score of anchors.
addStrandCombination    Add combination of anchor strand orientation.
cutoffBest10            Default optimal cutoff value of logistic
                        regression.
cutoffByTF              Optimal cutoff values for logistic regression
                        models.
getCisPairs             Build a 'GInteractions' object with all pairs
                        of input 'GRanges' within a given distance.
modelBest10Avg          Default parameters for logistic regression
                        model in sevenC.
motif.hg19.CTCF         CTCF motif locations in human genome hg19.
motif.hg19.CTCF.chr22   CTCF motif locations on chromosome 22 in human
                        genome hg19.
motif.hg19.CTCF.chr22.cov
                        CTCF motifs on human chromosome 22 with example
                        coverage.
parseLoopsRao           Parse chromatin loops from Rao et al. 2014 as
                        strict 'GInteractions'.
parseLoopsTang          Parse chromatin interactions from Tang et al.
                        2015 as 'GInteractions'.
predLogit               Predict interaction probability using logistic
                        regression model.
predLoops               Predict looping interactions.
prepareCisPairs         Prepares motif pairs as 'GInteractions' and add
                        genomic features.
sevenC                  Computational chromosome conformation capture
                        by correlation of ChIP-seq at CTCF motifs (7C)
TFspecificModels        TF specific parameters for logistic regression
                        in sevenC
