# Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

## Documentation for package ‘coMethDMR’ version 1.4.0

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

## Help Pages

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