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

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Documentation for package ‘sevenC’ version 1.7.0

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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