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| MEAL-package | MEAL (Methylation and Expression AnaLizer): Package for analysing methylation and expression data |
| AnalysisRegionResults | AnalysisRegionResults instances |
| analysisRegionResults | AnalysisRegionResults instances |
| AnalysisRegionResults-class | AnalysisRegionResults instances |
| AnalysisRegionResults-methods | AnalysisRegionResults instances |
| AnalysisResults | AnalysisResults instances |
| analysisResults | AnalysisResults instances |
| AnalysisResults-class | AnalysisResults instances |
| AnalysisResults-methods | AnalysisResults instances |
| blocks | AnalysisResults instances |
| blocks-method | AnalysisResults instances |
| bumps | AnalysisResults instances |
| bumps-method | AnalysisResults instances |
| calculateRelevantSNPs | Calculate the SNPs correlated to cpgs |
| computeRDAR2 | Compute signification of RDA test |
| correlationMethExprs | Computes the correlation between methylation and expression |
| covariableNames | AnalysisResults instances |
| covariableNames-method | AnalysisResults instances |
| 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 |
| Defunct | Computes the correlation between methylation and expression |
| dmrCate | AnalysisResults instances |
| dmrCate-method | AnalysisResults instances |
| explainedVariance | Calculate R2 for different variables |
| exportResults | Exports results data.frames to csv files. |
| exportResults-method | AnalysisResults instances |
| feats | AnalysisResults instances |
| feats-method | AnalysisResults instances |
| featvals | AnalysisResults instances |
| featvals-method | AnalysisResults instances |
| filterSet | Filter a 'MethylationSet', an 'ExpressionSet' or a 'SnpSet' |
| getGeneVals | Get all probes related to gene |
| getGeneVals-method | AnalysisResults instances |
| getMs-method | AnalysisResults instances |
| getRange | AnalysisRegionResults instances |
| getRange-method | AnalysisRegionResults instances |
| getRDA | AnalysisRegionResults instances |
| getRDA-method | AnalysisRegionResults instances |
| globalPval | AnalysisRegionResults instances |
| globalPval-method | AnalysisRegionResults instances |
| globalR2 | AnalysisRegionResults instances |
| globalR2-method | AnalysisRegionResults instances |
| MEAL | MEAL (Methylation and Expression AnaLizer): Package for analysing methylation and expression data |
| MEAL-defunct | Defunct functions |
| model | AnalysisResults instances |
| model-method | AnalysisResults instances |
| modelVariables | AnalysisResults instances |
| modelVariables-method | AnalysisResults instances |
| normalSNP | Normalize SNPs values |
| pData-method | AnalysisResults instances |
| pData<--method | AnalysisResults instances |
| phenoData-method | AnalysisResults instances |
| phenoData<--method | AnalysisResults instances |
| plotBestFeatures | Plot best n cpgs |
| plotEWAS | Plot a Manhattan plot with the probe results |
| plotEWAS-method | AnalysisResults instances |
| plotFeature | Plot values of a feature |
| plotLM | Plot a vector of R2 |
| plotQQ | QQ plot of probe analysis |
| plotQQ-method | AnalysisResults instances |
| plotRDA | Plot RDA results |
| plotRDA-method | AnalysisRegionResults instances |
| plotRegion | Plot of the region |
| plotRegion-method | AnalysisResults instances |
| plotRegionR2 | Plot R2 region values |
| plotRegionR2-method | AnalysisRegionResults instances |
| plotVolcano | Make a Volcano plot with the probe results |
| plotVolcano-method | AnalysisResults instances |
| preparePhenotype | Process a table of phenotypes |
| probeResults | AnalysisResults instances |
| probeResults-method | AnalysisResults instances |
| RDAPval | AnalysisRegionResults instances |
| RDAPval-method | AnalysisRegionResults instances |
| RDAset | Calculate RDA for a set |
| regionLM | AnalysisRegionResults instances |
| regionLM-method | AnalysisRegionResults instances |
| regionR2 | AnalysisRegionResults instances |
| regionR2-method | AnalysisRegionResults instances |
| regionResults | AnalysisResults instances |
| regionResults-method | AnalysisResults instances |
| sampleNames-method | AnalysisResults instances |
| snps | AnalysisRegionResults instances |
| snps-method | AnalysisRegionResults instances |
| snpsPvals | AnalysisRegionResults instances |
| snpsPvals-method | AnalysisRegionResults instances |
| snpsVar | AnalysisRegionResults instances |
| snpsVar-method | AnalysisRegionResults instances |
| topRDAhits | Get the top features associated with the RDA |
| topRDAhits-method | AnalysisRegionResults instances |
| variableNames | AnalysisResults instances |
| variableNames-method | AnalysisResults instances |