# Perform methylation analysis

## Documentation for package ‘MEAL’ version 1.8.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
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 | Exports results data.frames to csv files.
filterResults | Filter the data.frame obtained from probe analysis
filterSet | Filter a 'MethylationSet', an 'ExpressionSet' or a 'SnpSet'
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
plotBestFeatures | Plot best n cpgs
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'
preparePhenotype | Process a table of phenotypes
RDAset | Calculate RDA for a set
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