Familias: Inferring paternity and indentification based on DNA data
Familias has existed for a number of years as a Windows program for calculating probabilities in connection with using DNA data to infer family relationships. The code is now released in an R package.
| Package: | Familias |
| Type: | Package |
| Version: | 2.0 |
| Date: | 2014-07-17 |
| License: | GPL-2 |
| LazyLoad: | yes |
This package represents an implementation of an interface to the core Familias functions, which are programmed in C++. Note that this version, 2.0, implements a completely different interface to the core functions compared to the previous versions.
Petter Mostad <mostad@chalmers.se> and Thore Egeland <Thore.Egeland@gmail.com>
For more information, see www.familias.name
persons <- c("mother", "daughter", "AF")
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"))
par(mfrow=c(3,1))
plot(ped1);title("ped1, i.e., AF is father")
plot(ped2);title("ped2, i.e., AF is unrelated")
plot(ped3);title("ped3, i.e., AF is uncle")
par(mfrow=c(1,1))
mypedigrees <- list(isFather = ped1, unrelated=ped2, isUncle = ped3)
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)
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))
rownames(datamatrix) <- persons
FamiliasPosterior(mypedigrees, myloci, datamatrix)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.