set.K: Set covariance matrix for polygenic effect

In jendelman/GWASpoly: Genome-wide Association Studies for Autopolyploids

Set covariance matrix for polygenic effect

Description

Set covariance matrix for polygenic effect

Usage

set.K(data, K = NULL, n.core = 1, LOCO = NULL)

Arguments

data	Output from read.GWASpoly
K	Optional: user-supplied matrix
n.core	Number of cores for parallel computing
LOCO	TRUE/FALSE, whether to use leave-one-chromosome-out

Details

When LOCO = TRUE, K is computed for each chromosome as $K=MM'$, where M is the centered genotype matrix (lines x markers), and scaled to have unit diagonal (the overall scaling is not important for GWAS). When LOCO = FALSE, a single K matrix is computed for all markers (this was the original behavior of the function). Alternatively, the user can supply their own positive semidefinite K, with row.names that match the genotype identifiers (this option cannot be used with LOCO).

Value

Variable of class GWASpoly.K

jendelman/GWASpoly documentation built on Oct. 16, 2024, 5:59 a.m.