Familias2linkdat: Convert 'Familias' output to linkdat objects

Description

Familias is a widely used program for computations in forensic genetics. The function documented here facilitates the use of paramlink for specialized computations which are not implemented in Familias, e.g. conditional simulations.

The Familias program represents pedigrees and marker data in a way that differs from paramlink in several ways, mostly because of paramlink's stricter definition of a "pedigree". In paramlink, a pedigree must be connected, have numerical IDs, and each member must have either 0 or 2 parents present in the pedigree. None of this is required by FamiliasPedigree objects. The conversion function Familias2linkdat takes care of all of these potential differences: It converts each FamiliasPedigree into a list of connected linkdat objects, additional parents are added where needed, and non-numerical ID labels are stored in the plot.labels slot of the linkdat object(s).

Usage

Familias2linkdat(familiasped, datamatrix, loci)
connectedComponents(ID, FID, MID)

Arguments

familiasped

A Familias::FamiliasPedigree object or a list of such.

datamatrix

A data frame with two columns per marker (one for each allele) and one row per individual.

loci

A Familias::FamiliasLocus object or a list of such.

An integer vector: Individual ID.

FID

An integer vector: ID of father.

MID

An integer vector: ID of mother.

Value

A linkdat object, or a list of such.

References

Windows Familias is freely availabe from <https://familias.name>.

Examples

Run this code

# NOT RUN {
# Example
# }
# NOT RUN {
library(Familias)
data(NorwegianFrequencies)
locus1 = FamiliasLocus(NorwegianFrequencies$TH01)
persons <- c("mother", "daughter", "AF")
ped1 <- FamiliasPedigree(id=persons, dadid=c(NA, "AF", NA), momid=c(NA, "mother", NA), 
                         sex=c("female", "female", "male"))
datamatrix <- data.frame(THO1.1=c(NA, 8, NA), THO1.2=c(NA,9.3, NA))
rownames(datamatrix) = persons
x = Familias2linkdat(ped1, datamatrix, locus1)
plotPedList(list(x), new=TRUE, frametitles=c("H1"), available="shaded", marker = 1)

# Example
library(fam2r)
data(F21)
pedigrees = F21$pedigrees
datamatrix = F21$datamatrix
loci = F21$loci
x = Familias2linkdat(pedigrees, datamatrix, loci)
plotPedList(x, new=TRUE, frametitles=c("H1", "H2"), available="shaded")

# Give dev.width explicitly to allow for long names
plotPedList(x, new=TRUE, frametitles=c("H1", "H2"), available="shaded",
            dev.width=17)

# Numerical labels work better
plotPedList(x, new=TRUE, id.labels="num", frametitles=c("H1", "H2"),
            available="shaded")
# }