Function reference • coMethDMR

All functions
`AnnotateResults()`	Annotate `coMethDMR` Pipeline Results
`betaMatrix_ex1`	Alzheimer's Prefrontal Cortex (PFC) Methylation Data
`betaMatrix_ex2`	Alzheimer's Prefrontal Cortex (PFC) Methylation Data
`betaMatrix_ex3`	Alzheimer's Prefrontal Cortex (PFC) Methylation Data
`betaMatrix_ex4`	Alzheimer's Prefrontal Cortex (PFC) Methylation Data
`betasChr22_df`	Prefrontal Cortex (PFC) Methylation Data from Alzheimer's Disease subjects
`CloseBySingleRegion()`	Extract clusters of CpGs located closely in a genomic region.
`CoMethAllRegions()`	Extract contiguous co-methylated genomic regions from a list of pre-defined genomic regions
`CoMethSingleRegion()`	Wrapper function to find contiguous and comethyalted sub-regions within a pre-defined genomic region
`CpGsInfoAllRegions()`	Test Associations Between Regions and Phenotype
`CpGsInfoOneRegion()`	Test Associations Between a Region and Phenotype
`CreateParallelWorkers()`	Create a Parallel Computing Cluster
`CreateRdrop()`	Computes leave-one-out correlations (rDrop) for each CpG
`FindComethylatedRegions()`	Find Contiguous Co-Methylated Regions
`GetCpGsInRegion()`	Extract probe IDs for CpGs located in a genomic region
`GetResiduals()`	Get Linear Model Residuals
`ImportSesameData()`	Import Illumina manifests (sesameData versions)
`lmmTest()`	Fit mixed model to methylation values in one genomic region
`lmmTestAllRegions()`	Linear Mixed Models by Region
`MarkComethylatedCpGs()`	Mark CpGs in contiguous and co-methylated region
`MarkMissing()`	Return Column and Row Names of Samples and Probes under the Missingness Theshold
`NameRegion()`	Name a region with several CpGs based on its genomic location
`OrderCpGsByLocation()`	Order CpGs by genomic location
`pheno_df`	Example phenotype data file from Prefrontal Cortex (PFC) Methylation Data of Alzheimer's Disease subjects
`RegionsToRanges()`	Convert genomic regions in a data frame to GRanges format
`WriteCloseByAllRegions()`	Extract clusters of CpG probes located closely

Reference

All functions