gif: Kinship coefficient and genetic index of familiality

Description

The genetic index of familality is defined as the mean kinship between all pairs of individuals in a set multiplied by 100,000. Formally, it is defined as $$100,000 \times \frac{2}{n(n-1)}\sum_{i=1}^{n-1}\sum_{j=i+1}^n k_{ij}$$ where $n$ is the number of individuals in the set and $k_{ij}$ is the kinship coefficient between individuals $i$ and $j$.

The scaling is purely for convenience of presentation.

Usage

gif(data,gifset)

Arguments

data

the trio data of a pedigree

gifset

a subgroup of pedigree members

Value

The returned value is a list containing:

gifval

the genetic index of familiarity

References

Gholami K, Thomas A (1994) A linear time algorithm for calculation of multiple pairwise kinship coefficients and genetic index of familiality. Comp Biomed Res 27:342-350

Examples

Run this code

# NOT RUN {
test<-c(
 5,      0,      0,
 1,      0,      0,
 9,      5,      1,
 6,      0,      0,
10,      9,      6,
15,      9,      6,
21,     10,     15,
 3,      0,      0,
18,      3,     15,
23,     21,     18,
 2,      0,      0,
 4,      0,      0,
 7,      0,      0,
 8,      4,      7,
11,      5,      8,
12,      9,      6,
13,      9,      6,
14,      5,      8,
16,     14,      6,
17,     10,      2,
19,      9,     11,
20,     10,     13,
22,     21,     20)
test<-matrix(test,ncol=3,byrow=TRUE)
gif(test,gifset=c(20,21,22))

# all individuals
gif(test,gifset=1:23)
# }