Implementing custom mutation matrix

[Suhail Ghafoor]

Hi Ben,

I have a custom mutation matrix in 1x96 form that I'm attempting to convert to 4x64 form so I can use it as a mutationMatrix in initializeGenomicElementType() function. I have the new vector of 256 values that I converted to to 4x64 matrix however my sorted rows look different than the example described on Page 448 of the SLiM manual. In the manual, the rows are in the the following order:

AAA, AAC, AAG, AAT, ACA, ACC, ACG, ACT, AGA, AGG

However my sorted rows are in the following order:

AAA, AAC, AAG, AAT, ACA, ACC, ACG, ACT, AGA, AGC, AGG

The example in Chapter 24 does not clarify the sorting either, what could I be missing?

Thanks for the help in advance!

[Ben Haller]

Hi!  I'm not sure what you mean by "1x96 form".  However, I think the explanation for what you observe is simple: you have found a typo in the manual.  :->  The last item listed should of course be AGC, following the pattern previously established.  In other words, the rows essentially count upward in base 4, where A=0, C=1, G=2, and T=3, from row 000 (AAA) to row 333 (TTT), where 333 in base 4 is 63 in base 10.  I've fixed the typo for the next release of SLiM; sorry for the confusion!  (If there's something else going on here beyond the typo, or if I have gotten muddled in my answer – these things can be confusing – please do post again.  :->)  Thanks for the report.

Cheers,

-B.

Benjamin C. Haller

Messer Lab

Cornell University