MEAL: Perform methylation analysis
Version 1.6.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorCarlos Ruiz-Arenas [aut, cre], Carles Hernandez-Ferrer [aut], Juan R. González [aut]
Bioconductor views DNAMethylation Microarray Software WholeGenome
Date of publicationNone
MaintainerCarlos Ruiz-Arenas <carlos.ruiz@isglobal.org>
LicenseArtistic-2.0
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MEAL")

Man pages

AnalysisRegionResults-class: AnalysisRegionResults instances
AnalysisResults-class: AnalysisResults instances
calculateRelevantSNPs: Calculate the SNPs correlated to cpgs
computeRDAR2: Compute signification of RDA test
correlationMethExprs: Computes the correlation between methylation and expression
correlationMethSNPs: Computes the correlation between methylation and SNPs
createRanges: Create 'GenomicRanges' from data.frame
DAPipeline: Perform differential methylation analysis
DAProbe: Perform per probe analysis
DARegion: Detect regions differentially methylated
DARegionAnalysis: Analyse methylation or expression in a specific range
explainedVariance: Calculate R2 for different variables
exportResults-methods: Exports results data.frames to csv files.
filterSet-methods: Filter a 'MethylationSet', an 'ExpressionSet' or a 'SnpSet'
getGeneVals-methods: Get all probes related to gene
MEAL: MEAL (Methylation and Expression AnaLizer): Package for...
MEAL-defunct: Defunct functions
normalSNP: Normalize SNPs values
plotBestFeatures: Plot best n cpgs
plotEWAS-methods: Plot a Manhattan plot with the probe results
plotFeature: Plot values of a feature
plotLM: Plot a vector of R2
plotQQ-methods: QQ plot of probe analysis
plotRDA-methods: Plot RDA results
plotRegion-methods: Plot of the region
plotRegionR2-methods: Plot R2 region values
plotVolcano-methods: Make a Volcano plot with the probe results
prepareMethylationSet: Generating a 'MethylationSet'
preparePhenotype: Process a table of phenotypes
RDAset: Calculate RDA for a set
topRDAhits-methods: Get the top features associated with the RDA

Functions

AnalysisRegionResults Man page
AnalysisRegionResults-class Man page
AnalysisRegionResults-methods Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page
AnalysisResults Man page
AnalysisResults-class Man page
AnalysisResults-methods Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page Man page
DAPipeline Man page Source code
DAProbe Man page Source code
DARegion Man page Source code
DARegionAnalysis Man page Source code
MEAL Man page
MEAL-defunct Man page
MEAL-package Man page
RDAPval Man page
RDAPval,AnalysisRegionResults-method Man page
RDAset Man page Source code
SNPsforCPG Source code
analysisRegionResults Man page Source code
analysisResults Man page Source code
blocks Man page
blocks,AnalysisResults-method Man page
bumps Man page
bumps,AnalysisResults-method Man page
calculateRelevantSNPs Man page Source code
changeVectorType Source code
computeRDAR2 Man page Source code
correlationMethExprs Man page Source code
correlationMethSNPs Man page Source code
covariableNames Man page
covariableNames,AnalysisResults-method Man page
createModel Source code
createRanges Man page Source code
dmrCate Man page
dmrCate,AnalysisResults-method Man page
explainedVariance Man page Source code
exportResults Man page
exportResults,AnalysisResults-method Man page
feats Man page
feats,AnalysisResults-method Man page
featvals Man page
featvals,AnalysisResults-method Man page
filterResults Source code
filterSet Man page Source code
getCentroids Source code
getGeneVals Man page
getGeneVals,AnalysisResults-method Man page
getMs,AnalysisResults-method Man page
getRDA Man page
getRDA,AnalysisRegionResults-method Man page
getRange Man page
getRange,AnalysisRegionResults-method Man page
globalPval Man page
globalPval,AnalysisRegionResults-method Man page
globalR2 Man page
globalR2,AnalysisRegionResults-method Man page
model Man page
model,AnalysisResults-method Man page
modelVariables Man page
modelVariables,AnalysisResults-method Man page
normalSNP Man page Source code
pData,AnalysisResults-method Man page
pData<-,AnalysisResults,ANY-method Man page
phenoData,AnalysisResults-method Man page
phenoData<-,AnalysisResults,ANY-method Man page
plotBestFeatures Man page Source code
plotEWAS Man page
plotEWAS,AnalysisResults-method Man page
plotFeature Man page Source code
plotLM Man page Source code
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
plotVolcano Man page
plotVolcano,AnalysisResults-method Man page
prepareMethylationSet Man page Source code
preparePhenotype Man page Source code
probeResults Man page
probeResults,AnalysisResults-method Man page
qqplotBand Source code
regionR2 Man page
regionR2,AnalysisRegionResults-method Man page
regionResults Man page
regionResults,AnalysisResults-method Man page
sampleNames,AnalysisResults-method Man page
setResidues Source code
topRDAhits Man page
topRDAhits,AnalysisRegionResults-method Man page
variableNames Man page
variableNames,AnalysisResults-method Man page

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/0_AllClasses.R
R/1_AllGenerics.R
R/AnalysisRegionResults_Constructor.R
R/AnalysisRegionResults_SettersGetters.R
R/AnalysisRegionResults_plotRDA.R
R/AnalysisRegionResults_plotRegionR2.R
R/AnalysisRegionResults_show.R
R/AnalysisRegionResults_topRDAhits.R
R/AnalysisResults_Constructor.R
R/AnalysisResults_SettersGetters.R
R/AnalysisResults_exportResults.R
R/AnalysisResults_plotEWAS.R
R/AnalysisResults_plotQQ.R
R/AnalysisResults_plotRegion.R
R/AnalysisResults_plotVolcano.R
R/AnalysisResults_show.R
R/DAPipeline.R
R/DAProbe.R
R/DARegion.R
R/DARegionAnalysis.R
R/Defunct.R
R/MEAL.R
R/RDAset.R
R/SNPsforCPG.R
R/calculateRelevantSNPs.R
R/changeVectorType.R
R/computeRDAR2.R
R/correlationMethExprs.R
R/correlationMethSNPs.R
R/createModel.R
R/createRanges.R
R/explainedVariance.R
R/filterResults.R
R/filterSet.R
R/normalSNP.R
R/plotBestFeatures.R
R/plotFeature.R
R/plotLM.R
R/prepareMethylationSet.R
R/preparePhenotype.R
build
build/vignette.rds
inst
inst/NEWS.Rd
inst/doc
inst/doc/MEAL.R
inst/doc/MEAL.Rmd
inst/doc/MEAL.html
inst/doc/caseExample.R
inst/doc/caseExample.Rmd
inst/doc/caseExample.html
man
man/AnalysisRegionResults-class.Rd
man/AnalysisResults-class.Rd
man/DAPipeline.Rd
man/DAProbe.Rd
man/DARegion.Rd
man/DARegionAnalysis.Rd
man/MEAL-defunct.Rd
man/MEAL.Rd
man/RDAset.Rd
man/calculateRelevantSNPs.Rd
man/computeRDAR2.Rd
man/correlationMethExprs.Rd
man/correlationMethSNPs.Rd
man/createRanges.Rd
man/explainedVariance.Rd
man/exportResults-methods.Rd
man/filterSet-methods.Rd
man/getGeneVals-methods.Rd
man/normalSNP.Rd
man/plotBestFeatures.Rd
man/plotEWAS-methods.Rd
man/plotFeature.Rd
man/plotLM.Rd
man/plotQQ-methods.Rd
man/plotRDA-methods.Rd
man/plotRegion-methods.Rd
man/plotRegionR2-methods.Rd
man/plotVolcano-methods.Rd
man/prepareMethylationSet.Rd
man/preparePhenotype.Rd
man/topRDAhits-methods.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_01createSet.R
tests/testthat/test_02preparePhenotype.R
tests/testthat/test_03createModel.R
tests/testthat/test_04filters.R
tests/testthat/test_05probeAnalysis.R
tests/testthat/test_06regionAnalysis.R
tests/testthat/test_07pipeline.R
tests/testthat/test_08rangeAnalysis.R
tests/testthat/test_09explainedVariance.R
tests/testthat/test_10exportResults.R
tests/testthat/test_11plotting.R
tests/testthat/test_12RDA.R
tests/testthat/test_13SNPsCalculation.R
tests/testthat/test_14getGenes.R
tests/testthat/test_15correlationMethExpr.R
vignettes
vignettes/MEAL.Rmd
vignettes/caseExample.Rmd
vignettes/vignette.bib
MEAL documentation built on May 20, 2017, 9:28 p.m.