Man pages for gevaertlab/EpiMix
EpiMix: an integrative tool for the population-level analysis of DNA methylation
| addDistNearestTSS | Calculate the distance between probe and gene TSS |
| addGeneNames | The addGeneNames function |
| BatchCorrection_Combat | The BatchCorrection_Combat function |
| BatchCorrection_Seurat | The BatchCorrection_Seurat function |
| betaEst_2 | The betaEst_2 function |
| blc_2 | The blc_2 function |
| calcDistNearestTSS | Calculate distance from region to nearest TSS |
| ClusterProbes | The ClusterProbes function |
| ComBat_NoFiles | The ComBat_NoFiles function |
| combineForEachOutput | The combineForEachOutput function |
| convertAnnotToDF | The convertAnnotToDF function |
| convertGeneNames | The convertGeneNames function |
| CorrectBatchEffect | The CorrectBatchEffect function |
| dot-extractPriMiRNA | The extractPriMiRNA function |
| dot-getComp | The .getComp function |
| dot-getMetGroup | The .getMetGroup function |
| dot-mapProbeGene | The .mapProbeGene function |
| dot-splitMetData | The .splitMetData function |
| EpiMix | The EpiMix function |
| EpiMix_getInfiniumAnnotation | The EpiMix_getInfiniumAnnotation function |
| EpiMix_PlotGene | The EpiMix_PlotGene function |
| EpiMix_PlotModel | The EpiMix_PlotModel function. |
| EpiMix_PlotProbe | The EpiMix_PlotProbe function |
| EpiMix_PlotSurvival | EpiMix_PlotSurvival function |
| filterLinearProbes | The filterLinearProbes function |
| filterMethMatrix | The filterMethMatrix function |
| filterProbes | The filterProbes function |
| find_miRNA_targets | The find_miRNA_targets function |
| functionEnrich | The functionEnrich function |
| generateFunctionalPairs | The generateFunctionalPairs function |
| GEO_Download_DNAMethylation | The GEO_Download_DNAmethylation function |
| GEO_Download_GeneExpression | The GEO_Download_GeneExpression function |
| GEO_EstimateMissingValues_Methylation | The GEO_EstimateMissingValues_Methylation function |
| GEO_EstimateMissingValues_Molecular | The GEO_EstimateMissingValues_Molecular function |
| GEO_GetSampleInfo | The GEO_GetSampleInfo function |
| GEO_getSampleMap | the GEO_getSampleMap function |
| get.chromosome | The get.chromosome function |
| getFeatureProbe | getFeatureProbe to select probes within promoter regions or... |
| get_firehoseData | The get_firehoseData function |
| getFunctionalGenes | The getFunctionalGenes function |
| getLncRNAData | The getLncRNAData function |
| getMethStates | The getMethStates function |
| getMethStates_Helper | The getMethStates_Helper function |
| GetNearGenes | GetNearGenes to collect nearby genes for one locus. |
| get.prevalence | The get.prevalence function |
| getProbeAnnotation | The getProbeAnnotation function |
| Get.Pvalue.p | Calculate empirical Pvalue |
| getRandomGenes | The getRandomGenes function |
| getRegionNearGenes | Identifies nearest genes to a region |
| getRoadMapEnhancerProbes | getRoadMapEnhancerProbes |
| GetSurvivalProbe | The GetSurvivalProbe function |
| getTSS | getTSS to fetch GENCODE gene annotation (transcripts level)... |
| mapTranscriptToGene | mapTranscriptToGene |
| MethylMix_MixtureModel | The MethylMix_MixtureModel function |
| MethylMix_ModelSingleGene | The MethylMix_ModelSingleGene function |
| MethylMix_Predict | The MethylMix_Predict function |
| MethylMix_RemoveFlipOver | The MethylMix_RemoveFlipOver function |
| predictOneGene | The predictOneGene function |
| Preprocess_CancerSite_Methylation27k | The Preprocess_CancerSite_Methylation27k function |
| Preprocess_DNAMethylation | The Preprocess_DNAMethylation function |
| Preprocess_GeneExpression | The Preprocess_GeneExpression function |
| Preprocess_MAdata_Cancer | The Preprocess_MAdata_Cancer function |
| Preprocess_MAdata_Normal | The Preprocess_MAdata_Normal function |
| removeDuplicatedGenes | The removeDuplicatedGenes function |
| splitmatrix | The splitmatix function |
| TCGA_Download_DNAmethylation | The TCGA_Download_DNAmethylation function |
| TCGA_Download_GeneExpression | The TCGA_Download_GeneExpression function |
| TCGA_EstimateMissingValues_MolecularData | The TCGA_EstimateMissingValues_MolecularData function |
| TCGA_GENERIC_CheckBatchEffect | The TCGA_GENERIC_CheckBatchEffect function |
| TCGA_GENERIC_CleanUpSampleNames | The TCGA_GENERIC_CleanUpSampleNames function |
| TCGA_GENERIC_GetSampleGroups | The TCGA_GENERIC_GetSampleGroups function |
| TCGA_GENERIC_LoadIlluminaMethylationData | The TCGA_GENERIC_LoadIlluminaMethylationData function |
| TCGA_GENERIC_MergeData | The TCGA_GENERIC_MergeData function |
| TCGA_GENERIC_MET_ClusterProbes_Helper_ClusterGenes_with_hclust | The... |
| TCGA_GetData | The TCGA_GetData function |
| TCGA_GetSampleInfo | The TCGA_GetSampleInfo function |
| TCGA_Load_MethylationData | The TCGA_Load_MethylationData function |
| TCGA_Load_MolecularData | The TCGA_Load_MolecularData function |
| TCGA_Preprocess_DNAmethylation | The TCGA_Preprocess_DNAmethylation function |
| TCGA_Preprocess_GeneExpression | The TCGA_Preprocess_GeneExpression function |
| TCGA_Process_EstimateMissingValues | The TCGA_Process_EstimateMissingValues function |
| TCGA_Select_Dataset | The TCGA_Select_Dataset function |
| test_gene_expr | The test_gene_expr function |
| translateMethylMixResults | The translateMethylMixResults function |
| validEpigenomes | The validEpigenomes function |
