[BioC] snpStats reference allele used in genetic associations?

Francesca [guest] guest at bioconductor.org
Fri May 23 12:30:25 CEST 2014


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    


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