writeFam {pedFamilias}

Export ped objects to .fam

Description

This function produces a .fam file readable by the Familias software (Egeland et al., 2000), containing all input pedigrees, their marker data and mutation models. The option openFam = TRUE calls openFamilias() to open a fresh Familias session with the produced file loaded.

Usage

writeFam(
  ...,
  famfile = "ped.fam",
  params = NULL,
  dbOnly = FALSE,
  openFam = FALSE,
  FamiliasPath = NULL,
  verbose = TRUE
)

openFamilias(famfile = NULL, FamiliasPath = NULL, verbose = TRUE)

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.

params

A list of further parameters; see readFam() for valid entries. See also Details for default values.

dbOnly

A logical. If TRUE, no pedigree information is included; only the frequency database.

openFam

A logical. If TRUE, an attempt is made to open the produced .fam file in an external Familias session. Only available on Windows systems with a working Familias installation.

FamiliasPath

The path to the Familias executable. If empty, the following are tried in order: "Familias3.exe", "C:/Program Files (x86)/Familias3/Familias3.exe".

verbose

A logical, by default TRUE.

Details

The following parameters are applied by default, but may be adjusted with the params argument:

• version = "3.2.8"

• dvi = FALSE (for now the only valid option)

• dbName = "unknown"

• dbSize = 1000

• dropout = 0

• maf = 0

• theta = 0

The params argument should be a list similar to the params slot produced by readFam() with includeParams = TRUE. Single entries are recycled if needed. If params contains a vector dropout with dropout probabilities for certain pedigree members, it is converted into corresponding dropoutConsider and dropoutValue vectors (see Examples).

Value

The file name is returned invisibly.

References

Egeland et al. (2000). Beyond traditional paternity and identification cases. Selecting the most probable pedigree. Forensic Sci Int 110(1): 47-59.

See Also

readFam().

Examples

# Create pedigree with 2 markers
x = nuclearPed() |>
  addMarker(geno = c("2/2", "1/3", "2/3"), alleles = 1:3,
            afreq = c(.3,.3,.4), name = "M1")

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

# Read back in
y = readFam(tmp)

stopifnot(identical(x, y))


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

# Write and read
y2 = x2 |>
  writeFam(famfile = tempfile()) |>
  readFam()

stopifnot(identical(x2, y2))


### Read/write including detailed parameters
params = list(theta = 0.1, dbName = "myDB", dropout = c("3" = 0.01))
fam = writeFam(x2, famfile = tempfile(), params = params)

dat = readFam(fam, includeParams = TRUE)

# Pedigree is now in the `main` slot
stopifnot(identical(x2, dat$main))

# The `dropout` parameter is converted to (and is equivalent to):
dat$params$dropoutConsider
dat$params$dropoutValue


### Read/write frequency database

# Write database as fam file
dbfam = writeFam(x2, famfile = tempfile(), dbOnly = TRUE)

# Read back in: The result is a list of marker attributes
a = readFam(dbfam)

# Attach to a pedigree and write to a new file
z = singleton(1) |> setMarkers(locusAttributes = a)
dbfam2 = writeFam(z, famfile = tempfile(), dbOnly = TRUE)

stopifnot(identical(readLines(dbfam), readLines(dbfam2)))