5.2 years ago by
University of Washington
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
different effect allele. The output contains a "minor.allele" column
which will tell you whether allele A or B was the minor (tested)
in your sample. If the minor allele was B but the reference allele
A, then you would reverse the sign of "Stat" (beta) and take the
of the odds ratio to get the effect in terms of allele A.
Defining which allele to test is a somewhat arbitrary choice, and
the definition of A and B alleles for GWAS data is usually determined
the array manufacturer, we chose to use the minor allele for greater
consistency. (This is the same convention followed by PLINK, a
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?).
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
> -- output of sessionInfo():
> Sent via the guest posting facility at bioconductor.org.