MEAL: Perform methylation analysis

Share:

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.

Author
Carlos Ruiz [aut, cre], Carles Hernandez-Ferrer [aut], Juan R. Gonz<c3><a1>lez [aut]
Date of publication
None
Maintainer
Carlos Ruiz <carlos.ruiz@isglobal.org>
License
Artistic-2.0
Version
1.4.2

View on Bioconductor

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
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
preparePhenotype
Process a table of phenotypes
RDAset
Calculate RDA for a set
topRDAhits-methods
Get the top features associated with the RDA

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