MethylMix: MethylMix: Identifying methylation driven cancer genes.

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MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression.

Author
Olivier Gevaert
Date of publication
None
Maintainer
Olivier Gevaert <olivier.gevaert@gmail.com>
License
GPL-2
Version
1.8.0

View on Bioconductor

Man pages

MAcancer
Cancer Gene expression data of glioblastoma patients from the...
MAcancer_CDH1
Cancer Gene expression data of CDH1 for breast cancer...
METcancer
DNA methylation data from cancer tissue from glioblastoma...
METcancer_CDH1
DNA methylation data for CDH1 from the breast cancer TCGA...
MethylMix
Mixture model for DNA methylation data in cancer.
MethylMix_PlotModel
Plotting a mixture model for a gene.
METnormal
DNA methylation data from normal tissue from glioblastoma...
METnormal_CDH1
DNA methylation data for CDH1 from the breast cancer TCGA...

Files in this package

MethylMix/DESCRIPTION
MethylMix/NAMESPACE
MethylMix/R
MethylMix/R/MethylMix.R
MethylMix/build
MethylMix/build/vignette.rds
MethylMix/data
MethylMix/data/MAcancer.rda
MethylMix/data/MAcancer_CDH1.rda
MethylMix/data/METcancer.rda
MethylMix/data/METcancer_CDH1.rda
MethylMix/data/METnormal.rda
MethylMix/data/METnormal_CDH1.rda
MethylMix/inst
MethylMix/inst/News.Rd
MethylMix/inst/doc
MethylMix/inst/doc/MethylMix.R
MethylMix/inst/doc/MethylMix.Rnw
MethylMix/inst/doc/MethylMix.pdf
MethylMix/man
MethylMix/man/MAcancer.Rd
MethylMix/man/MAcancer_CDH1.Rd
MethylMix/man/METcancer.Rd
MethylMix/man/METcancer_CDH1.Rd
MethylMix/man/METnormal.Rd
MethylMix/man/METnormal_CDH1.Rd
MethylMix/man/MethylMix.Rd
MethylMix/man/MethylMix_PlotModel.Rd
MethylMix/vignettes
MethylMix/vignettes/MethylMix.Rnw