# Permutation-Based Analysis associating Conserved Differentially Methylated Elements Across Multiple Generations to a Treatment Effect

## Documentation for package ‘methylInheritance’ version 1.35.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

calculateSignificantLevel | Calculate significant level for hypo and hyper conserved elements
demoForTransgenerationalAnalysis | The methylation information from samples over three generations. Information for each generation is stored in a 'methylRawList' format (for demo purpose).
extractInfo | Extract the information specific to a subsection of the permutation analysis
loadAllRDSResults | Load all RDS files created by the permutation and observation analysis
loadConvergenceData | Load convergence information from RDS files
mergePermutationAndObservation | Merge the permutation results with the observation results.
methylInheritanceResults | All observed and permutation results formatted in a 'methylInheritanceResults' class (for demo purpose).
plotConvergenceGraph | Generate a graph showing the convergence for a permutation analysis
plotGraph | Generate a graph for a permutation analysis
print.methylInheritanceAllResults | Print a 'methylInheritanceAllResults' object
runObservation | Run a differential methylation analysis on multi-generational dataset
runPermutation | Run all permutations on the specified multi-generational dataset
samplesForTransgenerationalAnalysis | All samples information, formated by 'methylKit', in a 'methylRawList' format (for demo purpose).