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/Gen eticsBase.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 [[alternative HTML version deleted]]