Familias-package {Familias}

Familias: Inferring paternity and identification based on DNA data

Description

This package provides an R interface to the Windows program Familias (https://familias.no), for calculating probabilities in forensic family genetics. The core source code (in C++) of the Windows program is contained in the package.

Details

The main purpose of this package is to provide an R interface to the calculation of likelihood ratios (LRs) in Familias. For other forensic pedigree analyses and visualisations we recommend the 'pedsuite' packages: https://magnusdv.github.io/pedsuite/. In particular the package 'pedFamilias' facilitates conversion of .fam files into the 'pedsuite' format.

Author(s)

Petter Mostad <[e-mail]> and Thore Egeland <[e-mail]>.

References

For more information, see https://familias.name/.

Examples

persons <- c("mother", "daughter", "AF")

# Pedigrees
ped1 <- FamiliasPedigree(id = persons, 
                         dadid = c(NA, "AF", NA), 
                         momid = c(NA, "mother", NA), 
                         sex = c("female", "female", "male"))
                         
ped2 <- FamiliasPedigree(id = c(persons, "TF"), 
                         dadid = c(NA, "TF", NA, NA), 
                         momid = c(NA, "mother", NA, NA), 
                         sex = c("female", "female", "male", "male"))
                         
ped3 <- FamiliasPedigree(id = c(persons, "TF", "gf", "gm"), 
                         dadid = c(NA, "TF", "gf", "gf", NA, NA), 
                         momid = c(NA, "mother", "gm", "gm", NA, NA), 
                         sex = c("female", "female", "male", "male", "male", "female"))
op <- par(mfrow = c(1,3))
plot(ped1); title("ped1: AF is father")
plot(ped2); title("ped2: AF is unrelated")
plot(ped3); title("ped3: AF is uncle")
par(op)

mypedigrees <- list(isFather = ped1, unrelated=ped2, isUncle = ped3)

# Loci
locus1 <- FamiliasLocus(frequencies = c(0.1, 0.2, 0.3, 0.4), 
                        allelenames = c("A", "B", "C", "D"), 
                        name = "locus1")
locus2 <- FamiliasLocus(c(0.2, 0.3, 0.5), 
                        c(17, 18, 19), 
                        "loc2",
                        femaleMutationRate = 0.05)
myloci <- list(locus1, locus2)

# Genotype data
datamatrix <- data.frame(locus1.1 = c("A", "A", "A"), 
                         locus1.2 = c("B", "B", "C"), 
                         locus2.1 = c(17, 19, 19), 
                         locus2.2 = c(18, 18, 18), 
                         row.names = persons)

# Calculate LR
FamiliasPosterior(mypedigrees, myloci, datamatrix)