ABneutral: Run Model with no selection (ABneutral)

In jlab-code/AlphaBeta: Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants

Run Model with no selection (ABneutral)

Description

This model assumes that heritable gains and losses in cytosine methylation are selectively neutral.

Usage

ABneutral(pedigree.data, p0uu, eqp, eqp.weight, Nstarts, out.dir, out.name)

Arguments

pedigree.data	pedigree data.
p0uu	initial proportion of unmethylated cytosines.
eqp	equilibrium proportion of unmethylated cytosines.
eqp.weight	weight assigned to equilibrium function.
Nstarts	iterations for non linear LSQ optimization.
out.dir	output directory.
out.name	output file name.

Value

ABneutral RData file.

Examples

#Get some toy data
inFile <- readRDS(system.file("extdata/dm/","output.rds", package="AlphaBeta"))
pedigree <- inFile$Pdata
p0uu_in <- inFile$tmpp0
eqp.weight <- 1
Nstarts <- 2
out.name <- "CG_global_estimates_ABneutral"
out <- ABneutral(pedigree.data = pedigree,
                  p0uu=p0uu_in,
                  eqp=p0uu_in,
                  eqp.weight=eqp.weight,
                  Nstarts=Nstarts,
                  out.dir=getwd(),
                  out.name=out.name)

summary(out)

jlab-code/AlphaBeta documentation built on April 23, 2022, 11:02 a.m.