DMRMark: DMR Detection by Non-Homogeneous Hidden Markov Model from Methylation Array Data
Version 1.1.1

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.

AuthorLinghao SHEN <sl013@ie.cuhk.edu.hk>
Date of publication2017-04-21 17:58:43 UTC
MaintainerLinghao SHEN <sl013@ie.cuhk.edu.hk>
LicenseGPL
Version1.1.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DMRMark")

Getting started

Package overview

Popular man pages

BLCA: Single paired M-values of BLCA chr18 from TCGA
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...
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.
See all...

All man pages Function index File listing

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.

Functions

Files

NAMESPACE
data
data/BLCA.RData
R
R/boundFinder.R
R/DMRMark.R
R/MakeGSoptions.R
R/reformData.R
R/DMRViterbi.R
R/mvScatter.R
R/FullSampler.R
R/DMRMark_utils.R
MD5
DESCRIPTION
man
man/DMRViterbi.Rd
man/mvScatter.Rd
man/reformData.Rd
man/boundFinder.Rd
man/FullSample.Rd
man/DMRMark-package.Rd
man/DMRMark.Rd
man/BLCA.Rd
man/MakeGSoptions.Rd
DMRMark documentation built on May 20, 2017, 2:40 a.m.

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