DMR Detection by Non-Homogeneous Hidden Markov Model from Methylation Array Data


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Documentation for package ‘DMRMark’ version 1.1.1

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DMRMark-package DMR Detection by Non-Homogeneous Hidden Markov Model from Methylation Array Data
BLCA Single paired M-values of BLCA chr18 from TCGA
boundFinder Find a pair of reasonable distances of group means for hyper- and hypomethylation based on the quantile of two-group difference.
DMRMark Gibbs Sampler to estimate model parameters
DMRViterbi Viterbi algorithm to estimate posterior probabilities of DMRs.
FullSample Function implementing Gibbs Sampler with old-version interface
MakeGSoptions Encapsulate prior parameters and Gibbs Sampler (GS) control parameters
mvScatter Visualize the distributions of M-value pairs from differentially methylated CpG sites (DMC) or non-DMCs
reformData Reform M-values into a two-column matrix.