R: Run Model with no selection (ABneutral)

ABneutral {AlphaBeta}

R Documentation

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 <- system.file("extdata/dm/","pedigree.csv", package="AlphaBeta")
pedigree <- as.matrix(read.table(inFile, sep=",", header=TRUE, stringsAsFactors = FALSE))
p0uu_in <- 0.7435074
eqp.weight <- 1
Nstarts <- 2
output.data.dir <- paste0( getwd(),"/")
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=output.data.dir,
                  out.name=out.name)

summary(out)

[Package AlphaBeta version 1.1.0 Index]