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

## Documentation for package ‘EpiMix’ version 1.14.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## 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