R: Kinship coefficient and genetic index of familiality

gif {gap} | R Documentation

## 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 x 2/[n(n-1)]∑_(i=1)^(n-1)∑_(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

### Note

Adapted from gif.c, testable with -Dexecutable as standalone program, which can be use for any pair of indidivuals

### Author(s)

Alun Thomas, Jing Hua Zhao

### See Also

`pfc`

### Examples

    ## 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)

    ## End(Not run)

[Package gap version 1.2.3-1 Index]