# Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

## Documentation for package ‘sevenC’ version 1.6.0

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

## Help Pages

sevenC-package | Computational chromosome conformation capture by correlation of ChIP-seq at CTCF motifs (7C)
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.
getOutOfBound | Get out of chromosomal bound ranges.
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.
noZeroVar | returns indices of columns with non-zero variance
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)
slideMean | Sliding mean over x of intervals of size k
TFspecificModels | TF specific parameters for logistic regression in sevenC