MethylMix: MethylMix: Identifying methylation driven cancer genes

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. References: Gevaert 0. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8.

AuthorOlivier Gevaert
Date of publicationNone
MaintainerOlivier Gevaert <olivier.gevaert@gmail.com>
LicenseGPL-2
Version2.0.0

View on Bioconductor

Man pages

BatchData: BatchData data set

betaEst_2: The betaEst_2 function

blc_2: The blc_2 function

ClusterProbes: The ClusterProbes function

ComBat_NoFiles: The ComBat_NoFiles function

combineForEachOutput: The combineForEachOutput function

Download_DNAmethylation: The Download_DNAmethylation function

Download_GeneExpression: The Download_GeneExpression function

GEcancer: Cancer Gene expression data of glioblastoma patients from the...

GetData: The GetData function

get_firehoseData: The get_firehoseData function

METcancer: DNA methylation data from cancer tissue from glioblastoma...

MethylMix: MethylMix: Mixture model for DNA methylation data in cancer.

MethylMix_MixtureModel: The MethylMix_MixtureModel function

MethylMix_ModelGeneExpression: The MethylMix_ModelGeneExpression function

MethylMix_ModelSingleGene: The MethylMix_ModelSingleGene function

MethylMix_PlotModel: The MethylMix_PlotModel function.

MethylMix_RemoveFlipOver: The MethylMix_RemoveFlipOver function

METnormal: DNA methylation data from normal tissue from glioblastoma...

Preprocess_CancerSite_Methylation27k: The Preprocess_CancerSite_Methylation27k function

Preprocess_CancerSite_Methylation450k: The Preprocess_CancerSite_Methylation450k function

Preprocess_DNAmethylation: The Preprocess_DNAmethylation function

Preprocess_GeneExpression: The Preprocess_GeneExpression function

Preprocess_MAdata_Cancer: The Preprocess_MAdata_Cancer function

Preprocess_MAdata_Normal: The Preprocess_MAdata_Normal function

ProbeAnnotation: ProbeAnnotation data set

SNPprobes: SNPprobes data set

TCGA_BatchCorrection_MolecularData: The TCGA_BatchCorrection_MolecularData function

TCGA_GENERIC_BatchCorrection: The TCGA_GENERIC_BatchCorrection function

TCGA_GENERIC_CheckBatchEffect: The TCGA_GENERIC_CheckBatchEffect function

TCGA_GENERIC_CleanUpSampleNames: The TCGA_GENERIC_CleanUpSampleNames function

TCGA_GENERIC_GetSampleGroups: The TCGA_GENERIC_GetSampleGroups function

TCGA_GENERIC_LoadIlluminaMethylationData: The TCGA_GENERIC_LoadIlluminaMethylationData function

TCGA_GENERIC_MergeData: The TCGA_GENERIC_MergeData function

TCGA_GENERIC_MET_ClusterProbes_Helper_ClusterGenes_with_hclust: The...

TCGA_Load_MolecularData: The TCGA_Load_MolecularData function

TCGA_Process_EstimateMissingValues: The TCGA_Process_EstimateMissingValues function

Functions

BatchData Man page
betaEst_2 Man page
blc_2 Man page
ClusterProbes Man page
ComBat_NoFiles Man page
combineForEachOutput Man page
Download_DNAmethylation Man page
Download_GeneExpression Man page
GEcancer Man page
GetData Man page
get_firehoseData Man page
METcancer Man page
MethylMix Man page
MethylMix_MixtureModel Man page
MethylMix_ModelGeneExpression Man page
MethylMix_ModelSingleGene Man page
MethylMix_PlotModel Man page
MethylMix_RemoveFlipOver Man page
METnormal Man page
Preprocess_CancerSite_Methylation27k Man page
Preprocess_CancerSite_Methylation450k Man page
Preprocess_DNAmethylation Man page
Preprocess_GeneExpression Man page
Preprocess_MAdata_Cancer Man page
Preprocess_MAdata_Normal Man page
ProbeAnnotation Man page
SNPprobes Man page
TCGA_BatchCorrection_MolecularData Man page
TCGA_GENERIC_BatchCorrection Man page
TCGA_GENERIC_CheckBatchEffect Man page
TCGA_GENERIC_CleanUpSampleNames Man page
TCGA_GENERIC_GetSampleGroups Man page
TCGA_GENERIC_LoadIlluminaMethylationData Man page
TCGA_GENERIC_MergeData Man page
TCGA_GENERIC_MET_ClusterProbes_Helper_ClusterGenes_with_hclust Man page
TCGA_Load_MolecularData Man page
TCGA_Process_EstimateMissingValues Man page

Files

MethylMix/DESCRIPTION
MethylMix/NAMESPACE
MethylMix/R
MethylMix/R/ComBat_NoFiles.R MethylMix/R/Download_Preprocess.R MethylMix/R/MethylMix.R MethylMix/R/dataDoc.R
MethylMix/build
MethylMix/build/vignette.rds
MethylMix/data
MethylMix/data/BatchData.rda
MethylMix/data/GEcancer.rda
MethylMix/data/METcancer.rda
MethylMix/data/METnormal.rda
MethylMix/data/ProbeAnnotation.rda
MethylMix/data/SNPprobes.rda
MethylMix/data/datalist
MethylMix/inst
MethylMix/inst/News.Rd
MethylMix/inst/doc
MethylMix/inst/doc/vignettes.R
MethylMix/inst/doc/vignettes.Rmd
MethylMix/inst/doc/vignettes.html
MethylMix/man
MethylMix/man/BatchData.Rd MethylMix/man/ClusterProbes.Rd MethylMix/man/ComBat_NoFiles.Rd MethylMix/man/Download_DNAmethylation.Rd MethylMix/man/Download_GeneExpression.Rd MethylMix/man/GEcancer.Rd MethylMix/man/GetData.Rd MethylMix/man/METcancer.Rd MethylMix/man/METnormal.Rd MethylMix/man/MethylMix.Rd MethylMix/man/MethylMix_MixtureModel.Rd MethylMix/man/MethylMix_ModelGeneExpression.Rd MethylMix/man/MethylMix_ModelSingleGene.Rd MethylMix/man/MethylMix_PlotModel.Rd MethylMix/man/MethylMix_RemoveFlipOver.Rd MethylMix/man/Preprocess_CancerSite_Methylation27k.Rd MethylMix/man/Preprocess_CancerSite_Methylation450k.Rd MethylMix/man/Preprocess_DNAmethylation.Rd MethylMix/man/Preprocess_GeneExpression.Rd MethylMix/man/Preprocess_MAdata_Cancer.Rd MethylMix/man/Preprocess_MAdata_Normal.Rd MethylMix/man/ProbeAnnotation.Rd MethylMix/man/SNPprobes.Rd MethylMix/man/TCGA_BatchCorrection_MolecularData.Rd MethylMix/man/TCGA_GENERIC_BatchCorrection.Rd MethylMix/man/TCGA_GENERIC_CheckBatchEffect.Rd MethylMix/man/TCGA_GENERIC_CleanUpSampleNames.Rd MethylMix/man/TCGA_GENERIC_GetSampleGroups.Rd MethylMix/man/TCGA_GENERIC_LoadIlluminaMethylationData.Rd MethylMix/man/TCGA_GENERIC_MET_ClusterProbes_Helper_ClusterGenes_with_hclust.Rd MethylMix/man/TCGA_GENERIC_MergeData.Rd MethylMix/man/TCGA_Load_MolecularData.Rd MethylMix/man/TCGA_Process_EstimateMissingValues.Rd MethylMix/man/betaEst_2.Rd MethylMix/man/blc_2.Rd MethylMix/man/combineForEachOutput.Rd MethylMix/man/get_firehoseData.Rd
MethylMix/tests
MethylMix/tests/testthat
MethylMix/tests/testthat.R
MethylMix/tests/testthat/test_code.R
MethylMix/vignettes
MethylMix/vignettes/plot1.png
MethylMix/vignettes/plot2.png
MethylMix/vignettes/plot3.png
MethylMix/vignettes/plot4.png
MethylMix/vignettes/vignettes.Rmd

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