Man pages for TransBioInfoLab/coMethDMR
Accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies
| 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... |
| CloseBySingleRegion | Extract clusters of CpGs located closely in a genomic region. |
| CoMethAllRegions | Extract contiguous co-methylated genomic regions from a list... |
| coMethDMR_setup | Cache sesameData at Package Load |
| CoMethSingleRegion | Wrapper function to find contiguous and comethyalted... |
| CpGsInfoAllRegions | Test Associations Between Regions and Phenotype |
| CpGsInfoOneRegion | Test Associations Between a Region and Phenotype |
| CreateOutputDF | Create Output Dataframe |
| 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... |
| 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)... |
| RegionsToRanges | Convert genomic regions in a data frame to GRanges format |
| SplitCpGDFbyRegion | Split CpG dataframe by Subregion |
| WriteCloseByAllRegions | Extract clusters of CpG probes located closely |
