R help - May 2014 - snpStats reference allele used in genetic associations?

Hi,

Does anyone know how to find the reference allele used for genetic
associations ran in snpStats?

I have ran several associations using snp.rhs.tests, but I cannot tell which
allele was used as the "effect allele". Is it the one coded as
"Al1" in the
SNP.support file? I can find the RAF (risk allele frequency) from the
function col.summary, but again, which allele does this refer to? Also the
proportions of genotypes from the col.summary is given as "AA/AB/BB",
so I
cannot understand from that which is coded as the "risk" allele.

I could find this in the snpStats paper:
"For categorical variables, including SNPs, the user can reorder the
categories. The first one will be treated as reference category in the
analysis."

Thank you very much for your help!
Fra

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