AnnotateResults         Annotate 'coMethDMR' Pipeline Results
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)
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
RegionsToRanges         Convert genomic regions in a data frame to
                        GRanges format
WriteCloseByAllRegions
                        Extract clusters of CpG probes located closely
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
lmmTest                 Fit mixed model to methylation values in one
                        genomic region
lmmTestAllRegions       Linear Mixed Models by Region
pheno_df                Example phenotype data file from Prefrontal
                        Cortex (PFC) Methylation Data of Alzheimer's
                        Disease subjects
