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Generate a kinship matrix

Source: R/kinship.R
kinship.Rd

The function previously had an internal call to the kindepth function in order to provide the parameter pdepth (the generation number). This version requires the generation number to be calculated elsewhere and passed into the function.

Usage

kinship(id, father.id, mother.id, pdepth, sparse = FALSE)

Arguments

id

character vector of IDs for a set of animals.

father.id

character vector or NA for the IDs of the sires for the set of animals.

mother.id

character vector or NA for the IDs of the dams for the set of animals.

pdepth

integer vector indicating the generation number for each animal.

sparse

logical flag. If TRUE, Matrix::Diagnol() is used to make a unit diagonal matrix. If FALSE, base::diag() is used to make a unit square matrix.

Value

A kinship square matrix

Details

The rows (cols) of founders are just 0.5 * identity matrix, no further processing is needed for them. Parents must be processed before their children, and then a child's kinship is just a sum of the kinship's for his or her parents.

The code for the kinship function was written by Terry Therneau at the Mayo clinic and taken from his website. This function is part of a package written in S (and later ported to R) for calculating kinship and other statistics.

References

https://cran.r-project.org/package=kinship2

$Id: kinship.s,v 1.5 2003/01/04 19:07:53 therneau Exp $

Create the kinship matrix, using the algorithm of K Lange, Mathematical and Statistical Methods for Genetic Analysis, Springer, 1997, p 71-72.

Author

Terry M. Therneau, Mayo Clinic (mayo.edu), original version

All of the code on the original S-Plus kinship function (originally hosted on Terry Therneau's Mayo Clinic software page, offline since at least 2019) was stated to be released under the GNU General Public License (version 2 or later).

The R version became the kinship2 package available on CRAN:

as modified by M Raboin, 2014-09-08 14:44:26

Examples

library(nprcgenekeepr)
ped <- nprcgenekeepr::lacy1989Ped
ped$gen <- findGeneration(ped$id, ped$sire, ped$dam)
kmat <- kinship(ped$id, ped$sire, ped$dam, ped$gen)
ped
#>   id sire  dam gen population
#> 1  A <NA> <NA>   0       TRUE
#> 2  B <NA> <NA>   0       TRUE
#> 3  C    A    B   1       TRUE
#> 4  D    A    B   1       TRUE
#> 5  E <NA> <NA>   0       TRUE
#> 6  F    D    E   2       TRUE
#> 7  G    D    E   2       TRUE
kmat
#>       A     B     C    D    E     F     G
#> A 0.500 0.000 0.250 0.25 0.00 0.125 0.125
#> B 0.000 0.500 0.250 0.25 0.00 0.125 0.125
#> C 0.250 0.250 0.500 0.25 0.00 0.125 0.125
#> D 0.250 0.250 0.250 0.50 0.00 0.250 0.250
#> E 0.000 0.000 0.000 0.00 0.50 0.250 0.250
#> F 0.125 0.125 0.125 0.25 0.25 0.500 0.250
#> G 0.125 0.125 0.125 0.25 0.25 0.250 0.500