| MTK {GeneticSubsetter} | R Documentation |
MTK calculator
Description
This function calculates the Mean of Transformed Kinships (MTK) of a set of genotypes.
Usage
MTK(genos, subset, mat = NULL, power = 10)
Arguments
genos |
A matrix of genotypes, where each column is one individual, each row is one marker, and marker values are 1, 0, or -1, or NA, where 0 represents a heterozygous marker, and NA represents missing data. Note that this coding is different from the earlier MtkCalc, which cannot handle heterozygous markers. All data in this matrix must be numeric. |
subset |
A vector of genotype names for which to calculate MTK. |
mat |
A kinship matrix, if one has already been computed for the population. |
power |
The transformation that should be made to the kinship matrix, if the MTK criterion is used. If power=1, the kinship matrix is not transformed, if power=2, the kinship matrix is squared, etc. When the power is higher, this function preferentially eliminates genotypes that are closely related to other genotypes in the population. |
Value
The MTK of the specified subset.
Note
The ability to recognize heterozygous markers was included in MTK, resulting in a slightly different genotype coding scheme than the earlier MtkCalc.
Author(s)
Ryan C. Graebner
Examples
data(genotypes)
MTK(genotypes,subset=colnames(genotypes[1:5]))