[adegenet-forum] Converting genind object to genlight object

[Julian Wittische]

​Hello fellow *adegenet* users and contributors,

I would like to know if the way I converted a genind object to a genlight
object is the proper way, and why does the genlight object is more than
twice as big as the genind object, when the genlight-class purpose is among
others, to have a more efficient storage.

Is this discrepancy a signal I am doing something wrong?

I took only the allele count numbers of the second allele as suggested in
the " Formal "genlight-class" R documentation.

Code:

OMOgenind<-df2genind(OMOloc,ploidy=2,sep=",",NA.char="-9",type="codom",ind.names=make.unique(as.character(OMO[,1]),sep="sec"));

OMOgen<-OMOgenind at tab[,-seq(2,dim(OMOloc)[2],2),drop=FALSE]; # I take only
the second column (allele) for each locus.

OMOgenlight<-new("genlight",gen=OMOgen,ploidy=2,ind.names=make.unique(as.character(OMO[,1]),sep="sec"));

Output:


​

Have a nice day and thank you in advance,

Julian Wittische
PhD student
Université de Montréal

PS: I found issues with using the NA.char argument in df2genind() in the
previous version and found a lengthy custom fix so thank you very much for
fixing it in 2.0.1.

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