ABselectMMSOMA {AlphaBeta} | R Documentation

## 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)

[Package AlphaBeta version 1.2.3 Index]