from the documentation for read.snps.long

  For nucleotide coding, nucleotides are assigned to the nominal alleles
  in alphabetic order. Thus, for a SNP with either  "T" and "A"
  nucleotides in the variant position,
  the nominal genotypes AA, AB and BB will refer to A/A,
  A/T and T/T.

the maintainer may comment further.  in my view you would do well to keep
track of
the mapping by other means when using other input or construction methods.


On Fri, May 23, 2014 at 3:30 AM, Francesca [guest]
<guest@bioconductor.org>wrote:

> 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
>
>  -- output of sessionInfo():
>
> > sessionInfo()
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
> locale:
> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] snpStats_1.12.0 Matrix_1.1-0    survival_2.37-4
>
> loaded via a namespace (and not attached):
> [1] BiocGenerics_0.8.0 grid_3.0.2         lattice_0.20-24    parallel_3.0.2
>
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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