Closed TeresaPegan closed 3 years ago
Hi Teresa,
Yeah there is a non-documented feature in PCAngsd that you can turn on. :-) "-snp_weights"
Best, Jonas
Amazing! Thank you!
Just to make sure I understand the numbers properly: If I have 3 example SNPs with weights 0.04, 0, and -0.04, where 0.04 and -0.04 are close to the max and min weight in the whole dataset, my interpretation is that SNP 1 and SNP 2 are both contributing strongly to the pattern, but in opposite directions, and that SNP 2 with a weight of 0 is not contributing to the pattern?
Also, how do these weights apply to the different PCs? If a SNP has a strong weight, does that mean that it is contributing strongly to PC1, or might it be responsible for something in PC2 or one of the other PCs?
Thanks! -Teresa
Yeah exactly!
In the output each column will correspond to a different PC, where the number of columns is ether determined by PCAngsd or you can set it manually with the "-e" parameter. So If you only have one column then that is the SNP weights for only PC1.
Best, Jonas
Thanks!
Hello, Is there a way to get some kind of summary of PC loadings from PCANGSD? Or information about which sites are contributing the most strongly to the patterns? When I run PCANGSD on some of my data, I get an unexpected strong pattern in PC1 and I am trying to figure out what is causing it. It would be very helpful to know if the pattern is being caused by particular sites and/or a particular region of the chromosome. Thanks! -Teresa