In the package GWASTools, the function assocTestRegression performs an association test based on the minor allele. However this makes comparison across different datasets complicated because the minor allele in one population may be different from another. Is there a way to perform this test using the reference allele instead? Thanks, Danica -- output of sessionInfo(): -- Sent via the guest posting facility at bioconductor.org.

Hi Danica, There is not a way to change which allele is being tested in the code, but it is fairly straightforward to adjust the output to compare with a different effect allele. The output contains a "minor.allele" column which will tell you whether allele A or B was the minor (tested) allele in your sample. If the minor allele was B but the reference allele was A, then you would reverse the sign of "Stat" (beta) and take the inverse of the odds ratio to get the effect in terms of allele A. Defining which allele to test is a somewhat arbitrary choice, and since the definition of A and B alleles for GWAS data is usually determined by the array manufacturer, we chose to use the minor allele for greater consistency. (This is the same convention followed by PLINK, a popular tool for association testing.) Testing the reference allele would require additional information not contained in the dataset itself (which organism? which version of the reference sequence?). Stephanie On 8/12/14 2:37 AM, Danica [guest] wrote: > In the package GWASTools, the function assocTestRegression performs an association test based on the minor allele. However this makes comparison across different datasets complicated because the minor allele in one population may be different from another. > > Is there a way to perform this test using the reference allele instead? > > Thanks, > Danica > > -- output of sessionInfo(): > > > > -- > Sent via the guest posting facility at bioconductor.org. >