I have a 2x2 table of single nucleotide substitutions in DNA. The data rows represent the nucleotides in one genome (A) and columns are the nucleotides in the same positions of a different genome (B). The numbers are the times such substitution occurred.
A or T C or G A or T 3 12 C or G 12 3
I want to analyse whether these mutations are random. The problem is that since any "substitutions" to the same base (eg A->A) are not recorded you would expect to have twice as many substitutions from A/T to C/G than from A/T to A/T etc. The expected values for n=30:
A or T C or G A or T 5 10 C or G 10 5
Tests like chi-squared or Fisher's exact test determine if there are nonrandom associations between rows and columns. But I know that there is an association anyway and want to test whether the data is significantly different from it.
What statistical tests would be appropriate?
When performing chi-squared for independence is it possible to use specific expected values instead of using row and column totals?
Would it be correct to transform the data by dividing the A/T->C/G and C/G->A/T cells by 2, to get the mean number of substitutions to the other base category? The n would then change.