source("http://www.uvm.edu/~rsingle/Rdata/scripts_stat295F14.R")
 fms <- otherdata("FMS_small.tsv", sep="\t")
 attach(fms)

 x <- table(esr1_rs1042717,pre.BMI>25)
 x
 or.AA.GG <- (x[1,1]*x[3,2])/(x[1,2]*x[3,1])
 or.GA.GG <- (x[2,1]*x[3,2])/(x[2,2]*x[3,1])
 or.AA.GG  
 or.GA.GG

#swap the order of the columns (equivalent to the reciprocal of the above ORs)
 x <- table(esr1_rs1042717, !(pre.BMI>25) )
 x
 or.AA.GG <- (x[1,1]*x[3,2])/(x[1,2]*x[3,1])
 or.GA.GG <- (x[2,1]*x[3,2])/(x[2,2]*x[3,1])
 or.AA.GG  
 or.GA.GG

 chisq.test( table(esr1_rs1042717,pre.BMI>25) ,correct=F )