API for gevaertlab/EpiMix
EpiMix: an integrative tool for the population-level analysis of DNA methylation
| Global functions | |
|---|---|
| .extractPriMiRNA | Man page Source code |
| .getComp | Man page Source code |
| .getMetGroup | Man page Source code |
| .mapProbeGene | Man page Source code |
| .splitMetData | Man page Source code |
| BatchCorrection_Combat | Man page Source code |
| BatchCorrection_Seurat | Man page Source code |
| Beta.NA | Source code |
| ClusterProbes | Man page Source code |
| ComBat_NoFiles | Man page Source code |
| CorrectBatchEffect | Man page Source code |
| EpiMix | Man page Source code |
| EpiMix_GetData | Source code |
| EpiMix_PlotGene | Man page Source code |
| EpiMix_PlotModel | Man page Source code |
| EpiMix_PlotProbe | Man page Source code |
| EpiMix_PlotSurvival | Man page Source code |
| EpiMix_getInfiniumAnnotation | Man page Source code |
| GEO_Download_DNAMethylation | Man page Source code |
| GEO_Download_GeneExpression | Man page Source code |
| GEO_EstimateMissingValues_Methylation | Man page Source code |
| GEO_EstimateMissingValues_Molecular | Man page Source code |
| GEO_GetSampleInfo | Man page Source code |
| GEO_getSampleMap | Man page Source code |
| Get.Pvalue.p | Man page Source code |
| GetNearGenes | Man page Source code |
| GetSurvivalProbe | Man page Source code |
| L | Source code |
| MethylMix_MixtureModel | Man page Source code |
| MethylMix_ModelSingleGene | Man page Source code |
| MethylMix_Predict | Man page Source code |
| MethylMix_RemoveFlipOver | Man page Source code |
| Preprocess_CancerSite_Methylation27k | Man page Source code |
| Preprocess_DNAMethylation | Man page Source code |
| Preprocess_GeneExpression | Man page Source code |
| Preprocess_MAdata_Cancer | Man page Source code |
| Preprocess_MAdata_Normal | Man page Source code |
| TCGA_Download_DNAmethylation | Man page Source code |
| TCGA_Download_GeneExpression | Man page Source code |
| TCGA_EstimateMissingValues_MolecularData | Man page Source code |
| TCGA_GENERIC_CheckBatchEffect | Man page Source code |
| TCGA_GENERIC_CleanUpSampleNames | Man page Source code |
| TCGA_GENERIC_GetSampleGroups | Man page Source code |
| TCGA_GENERIC_LoadIlluminaMethylationData | Man page Source code |
| TCGA_GENERIC_MET_ClusterProbes_Helper_ClusterGenes_with_hclust | Man page Source code |
| TCGA_GENERIC_MergeData | Man page Source code |
| TCGA_GetData | Man page Source code |
| TCGA_GetSampleInfo | Man page Source code |
| TCGA_Load_MethylationData | Man page Source code |
| TCGA_Load_MolecularData | Man page Source code |
| TCGA_Preprocess_DNAmethylation | Man page Source code |
| TCGA_Preprocess_GeneExpression | Man page Source code |
| TCGA_Process_EstimateMissingValues | Man page Source code |
| TCGA_Select_Dataset | Man page Source code |
| addDistNearestTSS | Man page Source code |
| addGeneNames | Man page Source code |
| aprior | Source code |
| betaEst_2 | Man page |
| blc_2 | Man page |
| bprior | Source code |
| build.design | Source code |
| calcDistNearestTSS | Man page Source code |
| combineForEachOutput | Man page Source code |
| convertAnnotToDF | Man page Source code |
| convertGeneNames | Man page Source code |
| design.mat | Source code |
| filter.absent | Source code |
| filterLinearProbes | Man page Source code |
| filterMethMatrix | Man page Source code |
| filterProbes | Man page Source code |
| find_miRNA_targets | Man page Source code |
| functionEnrich | Man page Source code |
| generateFunctionalPairs | Man page Source code |
| get.chromosome | Man page Source code |
| get.prevalence | Man page Source code |
| getFeatureProbe | Man page |
| getFunctionalGenes | Man page Source code |
| getLncRNAData | Man page Source code |
| getMethStates | Man page Source code |
| getMethStates_Helper | Man page Source code |
| getProbeAnnotation | Man page Source code |
| getRandomGenes | Man page Source code |
| getRegionNearGenes | Man page Source code |
| getRoadMapEnhancerProbes | Man page Source code |
| getTSS | Man page |
| get_firehoseData | Man page Source code |
| int.eprior | Source code |
| it.sol | Source code |
| list.batch | Source code |
| listChromatinStates | Source code |
| listEpigenomces | Source code |
| mapTranscriptToGene | Man page Source code |
| postmean | Source code |
| postvar | Source code |
| predictOneGene | Man page Source code |
| removeDuplicatedGenes | Man page Source code |
| splitmatrix | Man page Source code |
| test_gene_expr | Man page Source code |
| translateMethylMixResults | Man page Source code |
| trim.dat | Source code |
| validEpigenomes | Man page Source code |
