ABselectMMSOMA: Model with selection against spontaneous gain of methylation...

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

Model with selection against spontaneous gain of methylation (outselectMM)

Description

This model assumes that somatically heritable gains of cytosine methylation are under negative selection.

Usage

ABselectMMSOMA(
  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

ABneutralSoma RData file.

Examples

#Get some toy data
inFile <- readRDS(system.file("extdata/soma/","outputSoma.rds", package="AlphaBeta"))
pedigree <- inFile$Pdata
p0uu_in <- inFile$tmpp0
eqp.weight <- 0.001
Nstarts <- 2
out.name <- "ABselectMMSOMA_CG_estimates"
out <- ABselectMMSOMA(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.