forrel (version 1.6.0)

writeFam: Convert ped objects to Familias format

Description

This function produces a .fam file readable by the Familias software, containing all input pedigrees and their marker data.

Usage

writeFam(..., famfile = "ped.fam", theta = 0)

Value

The filename is returned invisibly.

Arguments

...

One or several pedigrees. Each argument should be either a single ped object or a list of such. If the pedigrees are unnamed, they are assigned names "Ped 1", "Ped 2", etc.

famfile

The name or path to the output file to be written. The extension ".fam" is added if missing.

theta

A nonnegative number indicating a theta correction for the marker database. By default 0.

See Also

readFam()

Examples

library(pedprobr)

x = nuclearPed(father = "AF", mother = "MO", children = "CH") |>
  profileSim(N = 1, ids = c("AF", "CH"), seed = 111,
             markers = NorwegianFrequencies[1:2])

# Write to .fam
tmp = writeFam(x, famfile = tempfile())

# Read back in
y = readFam(tmp)

# Verify that likelihoods agree
stopifnot(all.equal(likelihood(x),
                    likelihood(y)))


### With stepwise mutation model
x2 = setMutmod(x, model = "stepwise",
               rate = list(male = 0.001, female = 0.002),
               range = 0.1, rate2 = 0.0001)

y2 = x2 |> writeFam(famfile = tempfile()) |> readFam()

stopifnot(all.equal(likelihood(x2), likelihood(y2)))