EpiMix: an integrative tool for the population-level analysis of DNA methylation


[Up] [Top]

Documentation for package ‘EpiMix’ version 1.9.0

Help Pages

.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