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


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Documentation for package ‘AlphaBeta’ version 1.0.0

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ABneutral Run Model with no selection (ABneutral)
ABneutralSOMA Model with no selection (outneutral)
ABnull Run model that considers no accumulation of epimutations (ABnull)
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
convertDMATRIX convertDMATRIX
dMatrix Constructing D-Matrices
FtestRSS Comparison of different models and selection of best model
makePHYLO Generating tree pedigree data
rc.meth.lvl Calculating rc.Meth.lvl