Description Usage Arguments Value Author(s) References See Also Examples
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.
1 | snpgrid(X, theta)
|
X |
A genotype matrix of n individuals with p SNPs (n \times p). |
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.
1 2 3 4 5 6 7 8 9 10 11 12 |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.