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

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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