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
