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!

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