glmmHeritability {SAIGEgds} | R Documentation |
Get the heritability estimate from the SAIGE model.
glmmHeritability(modobj, adjust=TRUE)
modobj |
an R object for SAIGE model parameters |
adjust |
if |
In SAIGE, penalized quasi-likelihood (PQL) is used to estimate the variance
component parameter tau. It is known to produce biased estimate of the variance
component tau using PQL. If adjust=TRUE
for binary outcomes, tau is
adjusted based prevalence and observed tau using the data in Supplementary
Table 7 (Zhou et al. 2018) to reduce the bias of PQL estimate of variance
component.
Return a liability scale heritability.
Xiuwen Zheng
# open a GDS file fn <- system.file("extdata", "grm1k_10k_snp.gds", package="SAIGEgds") gdsfile <- seqOpen(fn) # load phenotype phenofn <- system.file("extdata", "pheno.txt.gz", package="SAIGEgds") pheno <- read.table(phenofn, header=TRUE, as.is=TRUE) head(pheno) # fit the null model glmm <- seqFitNullGLMM_SPA(y ~ x1 + x2, pheno, gdsfile, trait.type="binary") glmmHeritability(glmm) seqClose(gdsfile)