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

View source: R/ABselectUUSOMA.R

ABselectUUSOMAR 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 <- readRDS(system.file("extdata/soma/","outputSoma.rds", package="AlphaBeta"))
pedigree <- inFile$Pdata
p0uu_in <- inFile$tmpp0
eqp.weight <- 0.001
Nstarts <- 2
out.name <- "ABselectUUSOMA_CG_estimates"
out <- ABselectUUSOMA(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.