Problem with read.Structure for fixed SNP loci

[biodray]

Hi,

I have noticed a problem with the function read.Structure, which doubled the number of row of the DataMatrix (YOUR_LIST_NAME$DataMatrix) compared to the number of individuals (as in YOUR_LIST_NAME$SampleID). I have encountered this problem with a dataset in which some loci were fixed.

This problem was caused by the structure_onehot internal function, which doesn't seem to manage fixed loci (keep only 1 colum for fixed loci and double the number rows).

Now that I have noticed it I had removed fixed loci, but maybe adding a warning, or modifying the way structure_onehot works migth prevent another person from problems with this package (which, by the way, I really like!).

[alexkychen]

Hi biodray. Sorry I missed your question. Do you still encounter the same problem?

[mgdesaix]

Just chiming in that this is still an issue as of assignPOP version 1.3.0. Fixed states mess up the input with read.Structure, such that the resulting genetic matrix has twice the number of individuals.