Smooth modeling of bisulfite sequencing

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Documentation for package ‘SOMNiBUS’ version 1.13.0

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

Help Pages

binomRegMethModel	A smoothed-EM algorithm to estimate covariate effects and test regional association in Bisulfite Sequencing-derived methylation data
binomRegMethModelPlot	Plot the smooth covariate effect
binomRegMethModelPred	A smoothed-EM algorithm to estimate covariate effects and test regional association in Bisulfite Sequencing-derived methylation data
binomRegMethModelSim	Simulate Bisulfite sequencing data from specified smooth covariate effects
binomRegMethPredPlot	Plot the predicted methylation levels
formatFromBismark	Parsing output from the Bismark alignment suite
formatFromBSmooth	Parsing output from the BSmooth alignment suite
formatFromBSseq	Parsing output from the BSseq package
RAdat	Methylation data from a rheumatoid arthritis study
RAdat2	A simulated methylation dataset based on a real data.
runSOMNiBUS	Wrapper function running the smoothed-EM algorithm to estimate covariate effects and test regional association in Bisulfite Sequencing-derived methylation data
splitDataByBed	Split methylation data into regions based on the genomic annotations
splitDataByChromatin	Split methylation data into regions based on the chromatin states
splitDataByDensity	Split methylation data into regions based on the density of CpGs
splitDataByGene	Split methylation data into regions based on the genes annotations
splitDataByGRanges	Split methylation data into regions based on the genomic annotations
splitDataByRegion	Split methylation data into regions based on the spacing of CpGs