Function reference • sevenC

Interactions
`prepareCisPairs()`	Prepares motif pairs as `GInteractions` and add genomic features.
`getCisPairs()`	Build a `GInteractions` object with all pairs of input `GRanges` within a given distance.
`addStrandCombination()`	Add combination of anchor strand orientation.
`addMotifScore()`	Add motif score of anchors.
`addInteractionSupport()`	Add column to `GInteractions` with overlap support.
`addCor()`	Add correlation of ChIP-seq coverage to motif pairs.
`addCovCor()`	Add correlation of anchor signals to pairs of close genomic regions.
Reading genomic data
`addCovToGR()`	Add coverage to regions in `GRanges` object.
`parseLoopsRao()`	Parse chromatin loops from Rao et al. 2014 as strict `GInteractions`.
`parseLoopsTang()`	Parse chromatin interactions from Tang et al. 2015 as `GInteractions`.
Prediction
`predLoops()`	Predict looping interactions.
Data sets
`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.
`modelBest10Avg`	Default parameters for logistic regression model in sevenC.
`TFspecificModels`	TF specific parameters for logistic regression in sevenC
`cutoffByTF`	Optimal cutoff values for logistic regression models.
`cutoffBest10`	Default optimal cutoff value of logistic regression.

Reference