# Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies

## Documentation for package ‘MethEvolSIM’ version 0.2

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

## Help Pages

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
computeFitch_islandGlbSt | Compute Fitch Parsimony for Global Methylation States at CpG Islands
compute_fitch | Compute Fitch Parsimony for Methylation Categories
compute_meanCor_i | Compute the Mean Correlation of Methylation State in Islands
compute_meanCor_ni | Compute the Mean Correlation of Methylation State in Non-islands
countSites_cherryMethDiff | Count Methylation Differences Between Cherry Pairs
count_upm | Count Methylation States
freqSites_cherryMethDiff | Compute Methylation Frequency Differences Between Cherry Pairs
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 Islands
get_islandSDFreqM | Calculate the Mean Standard Deviation of Methylated Sites in Islands
get_islandSDFreqP | Calculate the Mean Standard Deviation of Partially Methylated Sites in Islands
get_meanMeth_islands | Compute the Mean Methylation of CpG Islands
get_nonislandMeanFreqM | Calculate the Mean Frequency of Methylated Sites in Non-Islands
get_nonislandMeanFreqP | Calculate the Mean Frequency of Partially Methylated Sites in Non-Islands
get_nonislandSDFreqM | Calculate the Mean Standard Deviation of Methylated Sites in Non-Islands
get_nonislandSDFreqP | Calculate the Mean Standard Deviation of Partially Methylated Sites in Non-Islands
get_parameterValues | Get Default Parameter Values
get_siteFChange_cherry | Compute Site Frequency of Methylation Changes per Cherry
MeanSiteFChange_cherry | Compute the Mean Site Frequency of Methylation Changes per Cherry
mean_CherryFreqsChange_i | Mean Number of Significant Methylation Frequency Changes per Island in Cherries
mean_TreeFreqsChange_i | Mean Number of Significant Frequency Changes per Island Across all Tree Tips
pValue_CherryFreqsChange_i | Compute p-Values for Methylation Frequency Changes in Cherries
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 Computation
validate_structureIndices | Validate Structure Indices for Island and Non-Island Data
validate_tree | Validate and Parse a Phylogenetic Tree