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

Files in this package

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

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