Simulate DNA Methylation Dynamics on Different Genomic Structures along Genealogies

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Documentation for package ‘MethEvolSIM’ version 0.2.1

• 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