Dear experts, I have used snp.rhs.estimates in snpStats package and I am trying to get the normal statistics that is usually available using glm. I am able to get Estimate, S.E. and z-value (and derive p-values) from the list that results from snp.rhs.estimates, but I need the variance-covariance matrix, sigma, and intercept as well. Do you know how I can get this? This is an example dataset: X1 <- matrix(rbinom(1000,3,0.4),ncol=2) Y1 <- rnorm(500,apply(X1,1,sum),2) phenotype<- as.data.frame(Y1) colnames(phenotype)<- "phenotype" rx = matrix(as.raw(X1), nr=500) library(snpStats) sm = new("SnpMatrix", rx) lm1.sm <- snp.rhs.estimates(formula=as.formula("phenotype ~ 1"), family="gaussian", data=phenotype, snp.data=sm) Thank you in advance for your help! [[alternative HTML version deleted]]