Man pages for MEAL
Perform methylation analysis

AnalysisRegionResults-classAnalysisRegionResults instances
AnalysisResults-classAnalysisResults instances
calculateRelevantSNPsCalculate the SNPs correlated to cpgs
computeRDAR2Compute signification of RDA test
correlationMethExprsComputes the correlation between methylation and expression
correlationMethSNPsComputes the correlation between methylation and SNPs
createRangesCreate 'GenomicRanges' from data.frame
DAPipelinePerform differential methylation analysis
DAProbePerform per probe analysis
DARegionDetect regions differentially methylated
DARegionAnalysisAnalyse methylation or expression in a specific range
explainedVarianceCalculate R2 for different variables
exportResults-methodsExports results data.frames to csv files.
filterSet-methodsFilter a 'MethylationSet', an 'ExpressionSet' or a 'SnpSet'
getGeneVals-methodsGet all probes related to gene
MEALMEAL (Methylation and Expression AnaLizer): Package for...
MEAL-defunctDefunct functions
normalSNPNormalize SNPs values
plotBestFeaturesPlot best n cpgs
plotEWAS-methodsPlot a Manhattan plot with the probe results
plotFeaturePlot values of a feature
plotLMPlot a vector of R2
plotQQ-methodsQQ plot of probe analysis
plotRDA-methodsPlot RDA results
plotRegion-methodsPlot of the region
plotRegionR2-methodsPlot R2 region values
plotVolcano-methodsMake a Volcano plot with the probe results
prepareMethylationSetGenerating a 'MethylationSet'
preparePhenotypeProcess a table of phenotypes
RDAsetCalculate RDA for a set
topRDAhits-methodsGet the top features associated with the RDA
MEAL documentation built on May 31, 2017, 11:16 a.m.