Perform methylation analysis


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Documentation for package ‘MEAL’ version 1.10.1

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MEAL-package MEAL (Methylation and Expression AnaLizer): Package for analysing methylation and expression data
analysisRegionResults Old class to encapsulate results (deprecated in new version)
analysisResults Old class to encapsulate results (deprecated in new version)
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
DARegionAnalysis Analyse methylation or expression in a specific range
explainedVariance Calculate R2 for different variables
exportResults Exports results data.frames to csv files.
filterResults Filter the data.frame obtained from probe analysis
getGeneVals Get all probes related to a gene
getProbeResults Obtain probe results from a 'ResultSet'
getRDAresults Get a summary of RDA results
MEAL MEAL (Methylation and Expression AnaLizer): Package for analysing methylation and expression data
MEAL-defunct Defunct functions
normalSNP Normalize SNPs values
plotFeature Plot values of a feature
plotLM Plot a vector of R2
plotRDA Plot RDA results
plotRegion Plot results in a genomic region
prepareMethylationSet Generating a 'MethylationSet'
runBlockFinder Run blockFinder
runBumphunter Run bumphunter
runDiffMeanAnalysis Run differential mean analysis
runDiffVarAnalysis Run differential variance analysis
runDMRcate Run DMRcate
runPipeline Perform differential methylation analysis
runRDA Calculate RDA for a set
runRegionAnalysis Run different DMR detection methods
topRDAhits Get the top features associated with the RDA