ABselectUUSOMA {AlphaBeta} | R Documentation |
This model assumes that somatically heritable gains of cytosine methylation are under negative selection.
ABselectUUSOMA(pedigree.data, p0uu, eqp, eqp.weight, Nstarts, out.dir, out.name)
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. |
ABneutralSoma RData file.
## 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)