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

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Documentation for package ‘sevenC’ version 1.29.0

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

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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