Man pages for MEAL
Perform methylation analysis

analysisRegionResultsOld class to encapsulate results (deprecated in new version)
analysisResultsOld class to encapsulate results (deprecated in new version)
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
exportResultsExports results data.frames to csv files.
filterResultsFilter the data.frame obtained from probe analysis
filterSetFilter a 'MethylationSet', an 'ExpressionSet' or a 'SnpSet'
getGeneValsGet all probes related to a gene
getProbeResultsObtain probe results from a 'ResultSet'
getRDAresultsGet a summary of RDA results
MEALMEAL (Methylation and Expression AnaLizer): Package for...
MEAL-defunctDefunct functions
normalSNPNormalize SNPs values
plotBestFeaturesPlot best n cpgs
plotFeaturePlot values of a feature
plotLMPlot a vector of R2
plotRDAPlot RDA results
plotRegionPlot results in a genomic region
prepareMethylationSetGenerating a 'MethylationSet'
preparePhenotypeProcess a table of phenotypes
RDAsetCalculate RDA for a set
runBlockFinderRun blockFinder
runBumphunterRun bumphunter
runDiffMeanAnalysisRun differential mean analysis
runDiffVarAnalysisRun differential variance analysis
runDMRcateRun DMRcate
runPipelinePerform differential methylation analysis
runRDACalculate RDA for a set
runRegionAnalysisRun different DMR detection methods
topRDAhitsGet the top features associated with the RDA
MEAL documentation built on Nov. 17, 2017, 9:23 a.m.