Closed angelesdecara closed 5 years ago
Hi, Could you tell me which function of Loter you are using as the outputs can be different depending on the function (c.f. https://github.com/bcm-uga/Loter/blob/master/python-package/Local_Ancestry_Example.ipynb) ?
Could you paste a code example ?
Thanks
Sorry for my late reply. Here's the function I used:
res_loter=lc.loter_local_ancestry([Hnp02,Hnp03,Hnp04,Hnp05,Hnp06,Hnp07,Hnp08,Hnp09,Hnp10,Hnp11,Hnp12,Hnp13,Hnp14],Hnp01,num_threads=4)
Many thanks!
In this case, res_loter[0]
contains the inferred ancestries, being a matrix (as a numpy array) with haplotypes in rows and SNPs in columns, each entry between 0 and 12 identifies one of the 13 ref populations (respecting the index order of input); and res_loter[1]
contains the number of time that each ancestry was picked in the bagging procedure.
I hope that it will help.
Many thanks! That did the trick when saving it (using res_loter[0])!
You're welcome, do not hesitate if you have any questions.
Hi,
I'm trying to compare the results I have with RFmix and Loter, with one target population which may have received input from other 13 (I should have started somewhere simpler). When I try to save the output, it obviously complains either if I try with %i or %13i:
ValueError: Expected 1D or 2D array, got 3D array instead
what's the format of the output? i.e., what dimensions does res_loter have when using multiple populations? Sorry for my python ignorance...
Many thanks!