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

Perform differential analysis for methylation array data. Detect differentially methylated regions (DMRs) from array M-values. The core is a Non-homogeneous Hidden Markov Model for estimating spatial correlation and a novel Constrained Gaussian Mixture Model for modeling the M-value pairs of each individual locus.

Author
Linghao SHEN <sl013@ie.cuhk.edu.hk>
Date of publication
2016-09-04 20:14:25
Maintainer
Linghao SHEN <sl013@ie.cuhk.edu.hk>
License
GPL
Version
1.0

View on CRAN

Man pages

BLCA
Single paired M-values of BLCA chr18 from TCGA
boundFinder
Find a pair of reasonable distances of group means for hyper-...
DMRMark
Gibbs Sampler to estimate model parameters
DMRMark-package
DMR Detection by Non-Homogeneous Hidden Markov Model from...
DMRViterbi
Viterbi algorithm to estimate posterior probabilities of...
FullSample
Function implementing Gibbs Sampler with old-version...
MakeGSoptions
Encapsulate prior parameters and Gibbs Sampler (GS) control...
mvScatter
Visualize the distributions of M-value pairs from...
reformData
Reform M-values into a two-column matrix.

Files in this package

DMRMark
DMRMark/NAMESPACE
DMRMark/data
DMRMark/data/BLCA.RData
DMRMark/R
DMRMark/R/boundFinder.R
DMRMark/R/DMRMark.R
DMRMark/R/MakeGSoptions.R
DMRMark/R/reformData.R
DMRMark/R/DMRViterbi.R
DMRMark/R/mvScatter.R
DMRMark/R/FullSampler.R
DMRMark/R/DMRMark_utils.R
DMRMark/MD5
DMRMark/DESCRIPTION
DMRMark/man
DMRMark/man/DMRViterbi.Rd
DMRMark/man/mvScatter.Rd
DMRMark/man/reformData.Rd
DMRMark/man/boundFinder.Rd
DMRMark/man/FullSample.Rd
DMRMark/man/DMRMark-package.Rd
DMRMark/man/DMRMark.Rd
DMRMark/man/BLCA.Rd
DMRMark/man/MakeGSoptions.Rd