Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

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Documentation for package ‘AlphaBeta’ version 1.23.0

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

Help Pages

ABneutral	Run Model with no selection (ABneutral)
ABneutralSOMA	Model with no selection (outneutral)
ABnull	Run model that considers no accumulation of epimutations (ABnull)
ABplot	Plotting estimates
ABselectMM	Run model with selection against spontaneous gain of methylation (ABselectMM)
ABselectMMSOMA	Model with selection against spontaneous gain of methylation (outselectMM)
ABselectUU	Run model with selection against spontaneous loss of methylation (ABselectUU)
ABselectUUSOMA	Model with selection against spontaneous loss of methylation (outselectUU)
BOOTmodel	Bootstrap analysis with the best model
buildPedigree	Building Pedigree
dMatrix	Constructing D-Matrices
FtestRSS	Comparison of different models and selection of best model
plotPedigree	Plot Pedigree
rc.meth.lvl	Calculating rc.Meth.lvl