hypercube {dkDNA}R Documentation

Diffusion kernels on bi-allelic genotypes


This function construct a diffusion kernel on a p-dimensional hypercube, where each genotype takes on two possible configurations. This graph is obained by the p-Cartesian graph product of a complete graph K_2. It contains 2^p vertices corresponding to sequences of genotypes, and two vertices are adjacent if and only if just one SNP locus differs.


hypercube(X, theta)



A genotype matrix of n individuals with p bi-allelic genotypes (n \times p).


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

# create a genotype matrix of 5 individuals with 10 bi-allelic genotypes
X <- matrix(sample(c(0,1), 50, prob=c(0.6,0.4), replace=TRUE), ncol=10)

# set the rate of diffusion equal to 1
theta <- 1

# compute a hypercube kernel 
hypercube(X, theta)

[Package dkDNA version 0.1.1 Index]