[adegenet-forum] Missing values in genlight object

[Valeria Montano]

Dear Sara,

you can modify the @gen slot in the genlight object in this way and use it
to run the dudi.pca

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

I am very much sure there are smarter codes to do it but I tried it on the
flu dataset and it works :p
Hope this helps

Ciao
Valeria

On 10 January 2013 15:05, Thiho Jules <thjnant at gmail.com> wrote:

> Hello,
>
> I have created a genlight object within the package "adegenet". I wanted
> to do between-group PCA which requires that I first use the funtion,
> dudi.pca.
>
> But my genlight object involves "NA" or missing values, therefore, the
> dudi.pca function gives an error. I would like to know how I can remove the
> NA in a genlight object?
>
> I tried na.replace and na.omit but none works, and NA.posi only gives me
> the position of the missing values.
>
> Thank you in advance for your help,
> Best,
> Sara
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