Man pages for lissettegomez/coMethDMR
Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies

AnnotateResultsAnnotate 'coMethDMR' Pipeline Results
betaMatrix_ex1Alzheimer's Prefrontal Cortex (PFC) Methylation Data
betaMatrix_ex2Alzheimer's Prefrontal Cortex (PFC) Methylation Data
betaMatrix_ex3Alzheimer's Prefrontal Cortex (PFC) Methylation Data
betaMatrix_ex4Alzheimer's Prefrontal Cortex (PFC) Methylation Data
betasChr22_dfPrefrontal Cortex (PFC) Methylation Data from Alzheimer's...
CloseBySingleRegionExtract clusters of CpGs located closely in a genomic region.
CoMethAllRegionsExtract contiguous co-methylated genomic regions from a list...
CoMethSingleRegionWrapper function to find contiguous and comethyalted...
CpGsInfoAllRegionsTest associations of individual CpGs in multiple genomic...
CpGsInfoOneRegionTest associations of individual CpGs in a genomic region with...
CreateOutputDFCreate Output Dataframe
CreateParallelWorkersCreate a Parallel Computing Cluster
CreateRdropComputes leave-one-out correlations (rDrop) for each CpG
FindComethylatedRegionsFind contiguous comethylated regions based on output file...
GetCpGsInRegionExtract probe IDs for CpGs located in a genomic region
GetResidualsGet Residuals
lmmTestFit mixed model to methylation values in one genomic region
lmmTestAllRegionsFit mixed model to test association between a continuous...
MarkComethylatedCpGsMark CpGs in contiguous and co-methylated region
NameRegionName a region with several CpGs based on its genomic location
OrderCpGsByLocationOrder CpGs by genomic location
pheno_dfExample phenotype data file from Prefrontal Cortex (PFC)...
RegionsToRangesConvert genomic regions in a data frame to GRanges format
SplitCpGDFbyRegionSplit CpG dataframe by Subregion
WriteCloseByAllRegionsExtract clusters of CpG probes located closely
lissettegomez/coMethDMR documentation built on Oct. 15, 2019, 4:34 p.m.