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

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Documentation for package ‘EpiMix’ version 1.0.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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_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
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
GEO_Preprocess_DNAMethylation	The GEO_Preprocess_DNAMethylation function
GEO_Preprocess_GeneExpression	The GEO_Preprocess_GeneExpression 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
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