Familias-package: Familias: Inferring paternity and indentification based on...

In Familias: Probabilities for Pedigrees Given DNA Data

Description

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.

Details

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.

Author(s)

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

References

For more information, see www.familias.name

Examples

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)

Example output

Loading required package: kinship2
Loading required package: Matrix
Loading required package: quadprog
Loading required package: paramlink
Loading required package: Rsolnp
Did not plot the following people: AF 
$posterior
 isFather unrelated   isUncle 
0.4203139 0.2480877 0.3315984 

$prior
 isFather unrelated   isUncle 
0.3333333 0.3333333 0.3333333 

$LR
 isFather unrelated   isUncle 
1.0000000 0.5902439 0.7889306 

$LRperMarker
       isFather unrelated   isUncle
locus1        1 0.6000000 0.8000000
loc2          1 0.9837398 0.9861632

$likelihoods
    isFather    unrelated      isUncle 
5.535000e-06 3.267000e-06 4.366731e-06 

$likelihoodsPerSystem
       isFather unrelated     isUncle
locus1 0.000600  0.000360 0.000480000
loc2   0.009225  0.009075 0.009097356

Familias documentation built on May 2, 2019, 6:33 a.m.