Welcome to the first version of PCAdapt. genotype file must contain snps in rows and individuals in column. values are noted with 0, 1, 2 or 9 in case of missing data.
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To compile type:
$> make lapack $ > make -
To run PCAdapt:
$> ./PCAdapt //will display the manual if compilation went OK $ > ./PCAdapt -i Example/Data4pops_1 -o My4popsResults -K 5 -b 100 -s 200 //Will run an example with 400 individuals in 4 pops, and 8000 independent snps, where 400 of them are under selection. -
To run FastPCAdapt
$> ./PCAdapt fast //will display the manual if compilation went OK $ > ./PCAdapt fast -i Example/Data4pops_1 Example/Data4pops_2 -o My4popsResults -K 3 //Will run an example with 400 individuals in 4 pops, and 10000 independent snps in two different files, where 400 of them are under selection. -
To clean your folder from executable files:
$> make clean // removes the files in obj and PCAdapt $ > make realclean // removes the files in obj, obj_lapack, and PCAdapt
version 05/26/14: Computations of Bayes Factors, Posterior Odds, and conditionnal probabilities. Enhanced SVD initialisation. Potts model. Use of different values of Ck. scaling of the variables by default. Version of Fast PCAdapt!