Description Usage Arguments Details Examples
Fit a low-rank LMM on raw genotypes (no explicit scaling).
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y |
A vector of trait values (quantitative trait). |
X |
A matrix of covariates. The default value is matrix of ones for the intercept (one column). |
G |
A FBM matrix of genotypes. Missing values are not handled. |
cols |
A vector of columns of G to be used in the model. By default, all columns of G are used. |
M |
A scalar for normalization of the genetic relationship matrix: GRM = Z'Z / M, where Z is a matrix of standardized genotypes. By default, M = length(cols). |
K |
A matrix with the pre-computed cross-product Z'Z / M. By default, K = NULL, that means K is pre-computed inside the function. |
REML |
A boolean specifying the likelihood function, REML or ML. |
compute_mult |
A boolean enabling the computation of the effective sample size, when only model fitting is needed. The default value is TRUE. |
verbose |
The verbose level. The default value is 0 (verbose). |
The linear mixed model (LMM) is: y_i = X_i b + u_i + e_i, where
u ~ N(0, s2*h2*G) and e ~ N(0, s2 I)
var(y) = V = s2 * (h2*G + I)
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