qtl2 (version 0.32)

decomp_kinship: Calculate eigen decomposition of kinship matrix

Description

Calculate the eigen decomposition of a kinship matrix, or of a list of such matrices.

Usage

decomp_kinship(kinship, cores = 1)

Value

The eigen values and the transposed eigen vectors, as a list containing a vector values and a matrix vectors.

Arguments

kinship

A square matrix, or a list of square matrices.

cores

Number of CPU cores to use, for parallel calculations. (If 0, use parallel::detectCores().) Alternatively, this can be links to a set of cluster sockets, as produced by parallel::makeCluster().

Details

The result contains an attribute "eigen_decomp".

Examples

iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
iron <- iron[1:30,18:19] # subset to 30 individuals and two chromosomes
map <- insert_pseudomarkers(iron$gmap, step=1)
probs <- calc_genoprob(iron, map, error_prob=0.002)
K <- calc_kinship(probs)

Ke <- decomp_kinship(K)