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

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Documentation for package ‘methylInheritance’ version 1.32.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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).