[adegenet-forum] spatial pca with large SNP data

anne DaSilva anne_dasilva at hotmail.com
Fri Oct 16 19:02:13 CEST 2015


Dear all,
I would like to conduct a spatial PCA with 24000 SNP (after pruning). If I understand spca is not possible with a genlight object, so I use PLINK to recode my data in a STRUCTURE format, and then I work on a genind object in R....but the analysis ends....because of the size of the genind object I imagine.
Is there a solution (split the data? but how?)?
I am loosing all my hair over that problem (perhaps pathetically simple....)  and I would be really grateful if someone could help me to escape from my ignorance....
Kind regards
Anne



 Anne Blondeau Da Silva
 Unité de Génétique Moléculaire Animale
 UMR 1061 INRA-Université de Limoges
 Faculté des Sciences et Techniques
 123 Avenue Albert Thomas
 87060 LIMOGES Cedex
 Tél. 05 55 45 76 75
 Fax. 05 55 45 76 53
_______________________________________________
adegenet-forum mailing list
adegenet-forum at lists.r-forge.r-project.org
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum

_______________________________________________

adegenet-forum mailing list
adegenet-forum at lists.r-forge.r-project.org
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/adegenet-forum 		 	   		  
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20151016/67c750cd/attachment.html>


More information about the adegenet-forum mailing list