Dear All,





I have been using the LD() function to compute Linkage Disequilibrium on a geneSet. I was wondering how do I control which allele is read as 'A' v/s which allele is read as 'a' in the data (and for LD which allele correspondingly for 'B' and 'b').

In my analysis the sign of the D and r values are important, so I need to have a control on them.

 

[By 'A' and 'B' I am following the convention used in  page 12 of http://www.bioconductor.org/packages/2.4/bioc/manuals/GeneticsBase/man/GeneticsBase.pdf )

 

 

I am also wondering how the program does it, ie what the default mechanism is? My guess is that in constructing the pairwise haplotypes it has something to do with the allele/genotype frequencies. Can the authors please confirm?  

 

Thanks for your help,

--analabha

 

 

Analabha Basu

Institute for Human Genetics

UCSF 


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