fastGrmEVs {locStra} | R Documentation |
Computation of the k leading eigenvectors of the genomic relationship matrix, defined in Yang et al. (2011), for a (sparse) input matrix.
Description
Computation of the k leading eigenvectors of the genomic relationship matrix, defined in Yang et al. (2011), for a (sparse) input matrix.
Usage
fastGrmEVs(m, k, useCpp = TRUE, sparse = TRUE, robust = TRUE, q = 2)
Arguments
m |
A (sparse) matrix for which the eigenvectors of its genomic relationship matrix are sought. The input matrix is assumed to be oriented to contain the data for one individual per column. |
k |
The number of leading eigenvectors. |
useCpp |
Flag to switch between R or C++ implementations. Default is |
sparse |
Flag to switch between purpose-built dense or sparse implementations. Default is |
robust |
Flag to indicate if the classic ( |
q |
The number of power iteration steps (default is |
Value
The k leading eigenvectors of the genomic relationship matrix of m
as a column matrix.
References
Yang J, Lee SH, Goddard ME, Visscher PM (2011). GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet, 88(1):76-82.
N. Halko, P.G. Martinsson, and J.A. Tropp (2011). Finding Structure with Randomness: Probabilistic Algorithms for Constructing Approximate Matrix Decompositions. SIAM Review: 53(2), pp. 217–288.
Examples
require(locStra)
require(Matrix)
m <- matrix(sample(0:1,100,replace=TRUE),ncol=5)
sparseM <- Matrix(m,sparse=TRUE)
print(fastGrmEVs(sparseM,k=2,useCpp=FALSE))