I wanted to know about Plink's support for different organisms too, but could not find the information in the documentation. Looking at the source code was quicker:
grep -E 'define.+Chromosome' helper.cpp
So the answer to your question is no, unless you want to write some C++ to extend Plink. Looking into these functions, I found code for setting up the chromsomes in a 'par' (options) object.
To find where these are called from:
grep defineDogChromosomes *
plink.cpp: if (par::species_dog) defineDogChromosomes();
if (par::species_dog) defineDogChromosomes();
else if (par::species_sheep) defineSheepChromosomes();
else if (par::species_cow) defineCowChromosomes();
else if (par::species_horse) defineHorseChromosomes();
else if (par::species_rice) defineRiceChromosomes();
else if (par::species_mouse) defineMouseChromosomes();
You may be able to get away with writing one extra function, but I would also look at the code for the specific Plink analysis functions to see how your new scaffold definitions would be used.
modified 7.6 years ago
7.6 years ago by
iw9oel_ad ♦ 6.0k