MEAL: Perform methylation analysis

Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated.

AuthorCarlos Ruiz [aut, cre], Carles Hernandez-Ferrer [aut], Juan R. Gonz<c3><a1>lez [aut]
Date of publicationNone
MaintainerCarlos Ruiz <carlos.ruiz@isglobal.org>
LicenseArtistic-2.0
Version1.4.2

View on Bioconductor

Functions

analysisRegionResults Man page
AnalysisRegionResults Man page
AnalysisRegionResults-class Man page
AnalysisRegionResults-methods Man page
analysisResults Man page
AnalysisResults Man page
AnalysisResults-class Man page
AnalysisResults-methods Man page
blocks Man page
blocks,AnalysisResults-method Man page
bumps Man page
bumps,AnalysisResults-method Man page
calculateRelevantSNPs Man page
computeRDAR2 Man page
correlationMethExprs Man page
covariableNames Man page
covariableNames,AnalysisResults-method Man page
createRanges Man page
DAPipeline Man page
DAProbe Man page
DARegion Man page
DARegionAnalysis Man page
Defunct Man page
dmrCate Man page
dmrCate,AnalysisResults-method Man page
explainedVariance Man page
exportResults Man page
exportResults,AnalysisResults-method Man page
feats Man page
feats,AnalysisResults-method Man page
featvals Man page
featvals,AnalysisResults-method Man page
filterSet Man page
getGeneVals Man page
getGeneVals,AnalysisResults-method Man page
getMs,AnalysisResults-method Man page
getRange Man page
getRange,AnalysisRegionResults-method Man page
getRDA Man page
getRDA,AnalysisRegionResults-method Man page
globalPval Man page
globalPval,AnalysisRegionResults-method Man page
globalR2 Man page
globalR2,AnalysisRegionResults-method Man page
MEAL Man page
MEAL-defunct Man page
MEAL-package Man page
model Man page
model,AnalysisResults-method Man page
modelVariables Man page
modelVariables,AnalysisResults-method Man page
normalSNP Man page
pData<-,AnalysisResults,ANY-method Man page
pData,AnalysisResults-method Man page
phenoData<-,AnalysisResults,ANY-method Man page
phenoData,AnalysisResults-method Man page
plotBestFeatures Man page
plotEWAS Man page
plotEWAS,AnalysisResults-method Man page
plotFeature Man page
plotLM Man page
plotQQ Man page
plotQQ,AnalysisResults-method Man page
plotRDA Man page
plotRDA,AnalysisRegionResults-method Man page
plotRegion Man page
plotRegion,AnalysisResults-method Man page
plotRegionR2 Man page
plotRegionR2,AnalysisRegionResults-method Man page
plotVolcano Man page
plotVolcano,AnalysisResults-method Man page
preparePhenotype Man page
probeResults Man page
probeResults,AnalysisResults-method Man page
RDAPval Man page
RDAPval,AnalysisRegionResults-method Man page
RDAset Man page
regionLM Man page
regionLM,AnalysisRegionResults-method Man page
regionR2 Man page
regionR2,AnalysisRegionResults-method Man page
regionResults Man page
regionResults,AnalysisResults-method Man page
sampleNames,AnalysisResults-method Man page
snps Man page
snps,AnalysisRegionResults-method Man page
snpsPvals Man page
snpsPvals,AnalysisRegionResults-method Man page
snpsVar Man page
snpsVar,AnalysisRegionResults-method Man page
topRDAhits Man page
topRDAhits,AnalysisRegionResults-method Man page
variableNames Man page
variableNames,AnalysisResults-method Man page

Files

MEAL/DESCRIPTION
MEAL/NAMESPACE
MEAL/R
MEAL/R/0_AllClasses.R MEAL/R/1_AllGenerics.R MEAL/R/AnalysisRegionResults_Constructor.R MEAL/R/AnalysisRegionResults_SettersGetters.R MEAL/R/AnalysisRegionResults_plotRDA.R MEAL/R/AnalysisRegionResults_plotRegionR2.R MEAL/R/AnalysisRegionResults_show.R MEAL/R/AnalysisRegionResults_topRDAhits.R MEAL/R/AnalysisResults_Constructor.R MEAL/R/AnalysisResults_SettersGetters.R MEAL/R/AnalysisResults_exportResults.R MEAL/R/AnalysisResults_plotEWAS.R MEAL/R/AnalysisResults_plotQQ.R MEAL/R/AnalysisResults_plotRegion.R MEAL/R/AnalysisResults_plotVolcano.R MEAL/R/AnalysisResults_show.R MEAL/R/DAPipeline.R MEAL/R/DAProbe.R MEAL/R/DARegion.R MEAL/R/DARegionAnalysis.R MEAL/R/Defunct.R MEAL/R/MEAL.R MEAL/R/RDAset.R MEAL/R/SNPsforCPG.R MEAL/R/calculateRelevantSNPs.R MEAL/R/changeVectorType.R MEAL/R/computeRDAR2.R MEAL/R/correlationMethExprs.R MEAL/R/createModel.R MEAL/R/createRanges.R MEAL/R/explainedVariance.R MEAL/R/filterResults.R MEAL/R/filterSet.R MEAL/R/multiCorrMethExprs.R MEAL/R/normalSNP.R MEAL/R/plotBestFeatures.R MEAL/R/plotFeature.R MEAL/R/plotLM.R MEAL/R/preparePhenotype.R
MEAL/build
MEAL/build/vignette.rds
MEAL/inst
MEAL/inst/NEWS.Rd
MEAL/inst/doc
MEAL/inst/doc/MEAL.R
MEAL/inst/doc/MEAL.Rmd
MEAL/inst/doc/MEAL.html
MEAL/inst/doc/caseExample.R
MEAL/inst/doc/caseExample.Rmd
MEAL/inst/doc/caseExample.html
MEAL/man
MEAL/man/AnalysisRegionResults-class.Rd MEAL/man/AnalysisResults-class.Rd MEAL/man/DAPipeline.Rd MEAL/man/DAProbe.Rd MEAL/man/DARegion.Rd MEAL/man/DARegionAnalysis.Rd MEAL/man/MEAL-defunct.Rd MEAL/man/MEAL.Rd MEAL/man/RDAset.Rd MEAL/man/calculateRelevantSNPs.Rd MEAL/man/computeRDAR2.Rd MEAL/man/correlationMethExprs.Rd MEAL/man/createRanges.Rd MEAL/man/explainedVariance.Rd MEAL/man/exportResults-methods.Rd MEAL/man/filterSet-methods.Rd MEAL/man/getGeneVals-methods.Rd MEAL/man/normalSNP.Rd MEAL/man/plotBestFeatures.Rd MEAL/man/plotEWAS-methods.Rd MEAL/man/plotFeature.Rd MEAL/man/plotLM.Rd MEAL/man/plotQQ-methods.Rd MEAL/man/plotRDA-methods.Rd MEAL/man/plotRegion-methods.Rd MEAL/man/plotRegionR2-methods.Rd MEAL/man/plotVolcano-methods.Rd MEAL/man/preparePhenotype.Rd MEAL/man/topRDAhits-methods.Rd
MEAL/tests
MEAL/tests/testthat
MEAL/tests/testthat.R
MEAL/tests/testthat/test_02preparePhenotype.R
MEAL/tests/testthat/test_03createModel.R
MEAL/tests/testthat/test_04filters.R
MEAL/tests/testthat/test_05probeAnalysis.R
MEAL/tests/testthat/test_06regionAnalysis.R
MEAL/tests/testthat/test_07pipeline.R
MEAL/tests/testthat/test_08rangeAnalysis.R
MEAL/tests/testthat/test_09explainedVariance.R
MEAL/tests/testthat/test_10exportResults.R
MEAL/tests/testthat/test_11plotting.R
MEAL/tests/testthat/test_12RDA.R
MEAL/tests/testthat/test_13SNPsCalculation.R
MEAL/tests/testthat/test_14getGenes.R
MEAL/tests/testthat/test_15correlationMethExpr.R
MEAL/vignettes
MEAL/vignettes/MEAL.Rmd
MEAL/vignettes/caseExample.Rmd
MEAL/vignettes/vignette.bib

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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