pca selection statistic

[rachelzoeb]

I am having trouble calculating the PCA selection statistics described in Galinsky 2016 Fast PCA paper using the Eigensoft software.

In EIG v6.1.4 there appears to be a parameter file example.pcaselection.par and the output example.pcaselection.chisq but I’m unable to figure out how to run and produce this output. I have been unable to locate information about the selection statistic (pcaselection) in the README files (both in POPGEN and EIGENSOFT). It does say that “pcaselection was omitted from 6.1.3 by accident" but I don’t see any mention of it besides the example output in 6.1.4.

Have the names of this function changed? Could you point me to the explanation of how to run and generate the selection statistics using the pre-computed eigenvectors?

Any help is greatly appreciated,

Rachel Blumhagen

[kgalinsky]

Hi Rachel,

In the bin directory, do you have the pcaselection executable? You need to edit the example.pcaselection.par file to point at your geno/snp/ind file as well as the eigenvector file you generated with smartpca. You should also specify where you want the output to go. You then run "pcaselection -p <par file name>"

Best,
Kevin

[rachelzoeb]

Hi Kevin, I do have a pcaselection executable. I will try that, thank you! Rachel

…

On Nov 22, 2017, at 1:16 PM, Kevin Galinsky ***@***.***> wrote: Hi Rachel, In the bin directory, do you have the pcaselection executable? You need to edit the example.pcaselection.par file to point at your geno/snp/ind file as well as the eigenvector file you generated with smartpca. You should also specify where you want the output to go. You then run "pcaselection -p " Best, Kevin — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#21 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIdatdYNF-mvav0W_40CXWzDPupmxrjgks5s5IExgaJpZM4Qn71->.