snpgrid {dkDNA} | R Documentation |
This function construct a diffusion kernel on a p
-dimensional SNP grid
graph, where each genotype takes on three possible configurations, namely 0
('aa'), 1 ('Aa'), and 2('AA'). This graph is obained by the p
-Cartesian graph product of a path graph 0-1-2.
It contains 3^p
vertices corresponding to sequences of
genotypes, and two vertices are adjacent if and only if just one SNP
locus differs by 1.
snpgrid(X, theta)
X |
A genotype matrix of |
theta |
The rate of diffusion. |
Diffusion kernel matrix of size n \times n
.
This can be viewed as a covariance among individuals given the
diffusion rate.
Gota Morota morota@unl.edu and Masanori Koyama koyama.masanori@gmail.com
Kondor R and Lafferty J: (2002) Diffusion Kernels on Graphs and Other Discrete Input Spaces. ICML.
Morota G, Koyama M, Rosa GJM, Weigel KA, and Gianola D. (2013). Predicting complex traits using a diffusion kernel on genetic markers with an application to dairy cattle and wheat data. Genetics Selection Evolution. 45:17.
# set a seed
set.seed(4321)
# create a genotype matrix of 5 individuals with 10 SNPs
X <- matrix(sample(c(0,1,2), 50, prob=c(0.35, 0.3, 0.35), replace=TRUE),
ncol=10)
# set the rate of diffusion equal to 1
theta <- 1
# compute a SNP grid kernel
snpgrid(X, theta)