R: Model with selection against spontaneous loss of methylation...

ABselectUUSOMA {AlphaBeta}

R Documentation

Model with selection against spontaneous loss of methylation (outselectUU)

Description

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

Usage

ABselectUUSOMA(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 <- system.file("extdata/soma/","pedigreeSoma.csv", package="AlphaBeta")
pedigree <- as.matrix(read.table(inFile, sep=",", header=TRUE, stringsAsFactors = FALSE))
p0uu_in <- 0.54755
eqp.weight <- 0.001
Nstarts <- 2
output.data.dir <- paste0( getwd(),"/")
out.name <- "ABselectUUSOMA_CG_estimates"
out <- ABselectUUSOMA(pedigree.data = pedigree,
                  p0uu=p0uu_in,
                  eqp=p0uu_in,
                  eqp.weight=eqp.weight,
                  Nstarts=Nstarts,
                  out.dir=output.data.dir,
                  out.name=out.name)

summary(out)

[Package AlphaBeta version 1.1.0 Index]