[adegenet-forum] Between group PCA with genlight object

[Thiho Jules]

Hello,

I have a genlight object (the genlight object has been created with 
plink.raw file using the command "recodeA", I want to use the functions 
"dudi.pca" and "bca" to perform a between group PCA.

I have received this code from Valeria to replace the missing values with 0:

mydf<-lapply(your_genlight at gen, as.integer)
myrepl<-do.call(rbind, lapply(mydf, function(e) replace(e, is.na 
<http://is.na>(e), 0)))
dudi.pca(myrepl)

This code indeed works and I can perform dudi.pca and bca, but I was 
wondering whether this is correct to replace the missing values with 0 
as zero itself exists in the plink.raw for the markers with no second 
allele.

Thank you very much in advance,
Best,
Sara

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