.extractPriMiRNA | The extractPriMiRNA function |
addDistNearestTSS | Calculate the distance between probe and gene TSS |
addGeneNames | The addGeneNames function |
calcDistNearestTSS | Calculate distance from region to nearest TSS |
ClusterProbes | The ClusterProbes 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 |
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_GetSampleInfo | The GEO_GetSampleInfo function |
GEO_getSampleMap | the GEO_getSampleMap function |
Get.Pvalue.p | Calculate empirical Pvalue |
getFeatureProbe | getFeatureProbe to select probes within promoter regions or distal regions. |
getMethStates_Helper | The getMethStates_Helper function |
GetNearGenes | GetNearGenes to collect nearby genes for one locus. |
getProbeAnnotation | The getProbeAnnotation function |
getRegionNearGenes | Identifies nearest genes to a region |
GetSurvivalProbe | The GetSurvivalProbe function |
getTSS | getTSS to fetch GENCODE gene annotation (transcripts level) from Bioconductor package biomaRt If upstream and downstream are specified in TSS list, promoter regions of GENCODE gene will be generated. |
MethylMix_Predict | The MethylMix_Predict function |
predictOneGene | The predictOneGene function |
Preprocess_DNAMethylation | The Preprocess_DNAMethylation function |
Preprocess_GeneExpression | The Preprocess_GeneExpression function |
removeDuplicatedGenes | The removeDuplicatedGenes function |
TCGA_Download_DNAmethylation | The TCGA_Download_DNAmethylation function |
TCGA_Download_GeneExpression | The TCGA_Download_GeneExpression function |
TCGA_GetData | The TCGA_GetData function |
TCGA_GetSampleInfo | The TCGA_GetSampleInfo function |
TCGA_Preprocess_DNAmethylation | The TCGA_Preprocess_DNAmethylation function |
TCGA_Preprocess_GeneExpression | The TCGA_Preprocess_GeneExpression function |
TCGA_Select_Dataset | The TCGA_Select_Dataset function |
translateMethylMixResults | The translateMethylMixResults function |
validEpigenomes | The validEpigenomes function |