ABselectMM: Run model with selection against spontaneous gain of...

View source: R/ABselectMM.R

ABselectMMR Documentation

Run model with selection against spontaneous gain of methylation (ABselectMM)

Description

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

Usage

ABselectMM(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

nweight assigned to equilibrium function.

Nstarts

iterations for non linear LSQ optimization.

out.dir

output directory.

out.name

output file name.

Value

ABselectMM 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_ABselectMM"
out <- ABselectMM(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.