Man pages for MethEvolSIM
Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies
| categorize_islandGlbSt | Categorize Global States of CpG Islands |
| categorize_siteMethSt | Categorize Methylation Frequencies Based on Thresholds |
| cftpStepGenerator | cftpStepGenerator |
| combiStructureGenerator | combiStructureGenerator |
| compare_CherryFreqs | Compare Methylation Frequencies Between Two Tips |
| compute_fitch | Compute Fitch Parsimony for Methylation Categories |
| computeFitch_islandGlbSt | Compute Fitch Parsimony for Global Methylation States at CpG... |
| compute_meanCor_i | Compute the Mean Correlation of Methylation State in Islands |
| compute_meanCor_ni | Compute the Mean Correlation of Methylation State in... |
| countSites_cherryMethDiff | Count Methylation Differences Between Cherry Pairs |
| count_upm | Count Methylation States |
| freqSites_cherryMethDiff | Compute Methylation Frequency Differences Between Cherry... |
| get_cherryDist | Get Cherry Pair Distances from a Phylogenetic Tree |
| get_islandMeanFreqM | Calculate the Mean Frequency of Methylated Sites in Islands |
| get_islandMeanFreqP | Calculate the Mean Frequency of Partially Methylated Sites in... |
| get_islandSDFreqM | Calculate the Mean Standard Deviation of Methylated Sites in... |
| get_islandSDFreqP | Calculate the Mean Standard Deviation of Partially Methylated... |
| get_meanMeth_islands | Compute the Mean Methylation of CpG Islands |
| get_nonislandMeanFreqM | Calculate the Mean Frequency of Methylated Sites in... |
| get_nonislandMeanFreqP | Calculate the Mean Frequency of Partially Methylated Sites in... |
| get_nonislandSDFreqM | Calculate the Mean Standard Deviation of Methylated Sites in... |
| get_nonislandSDFreqP | Calculate the Mean Standard Deviation of Partially Methylated... |
| get_parameterValues | Get Default Parameter Values |
| get_siteFChange_cherry | Compute Site Frequency of Methylation Changes per Cherry |
| mean_CherryFreqsChange_i | Mean Number of Significant Methylation Frequency Changes per... |
| MeanSiteFChange_cherry | Compute the Mean Site Frequency of Methylation Changes per... |
| mean_TreeFreqsChange_i | Mean Number of Significant Frequency Changes per Island... |
| pValue_CherryFreqsChange_i | Compute p-Values for Methylation Frequency Changes in... |
| simulate_evolData | Simulate Data Evolution along a Tree |
| simulate_initialData | Simulate Initial Data |
| singleStructureGenerator | singleStructureGenerator |
| treeMultiRegionSimulator | treeMultiRegionSimulator |
| validate_dataAcrossTips | Validate Data Structure Across Tips |
| validate_data_cherryDist | Validate Structure of Input Data for Cherry Distance... |
| validate_structureIndices | Validate Structure Indices for Island and Non-Island Data |
| validate_tree | Validate and Parse a Phylogenetic Tree |
