[adegenet-forum] trouble accessing @other

[Zhian Kamvar]

Just to pop in here: This looks like a situation that is best solved by
using the strata slot.

> I want to subset part of the individuals of my genlight object according
> to a variable stored in the @other slot. I get an error I don't
understand.
> I stored 3 categorical variables in the @other slot. It looks like that:
> *> str(other(asocial.gl <http://asocial.gl>))*
> List of 3
>  $ basin : Factor w/ 3 levels "Rhine","Rhone_Valais",..: NA 2 NA 2 2 2 2 2
> 2 2 ...
>  $ Sgeno : Factor w/ 3 levels "mm","mp","pp": 1 2 3 1 1 1 1 1 1 1 ...
>  $ Spheno: Factor w/ 2 levels "M","P": 1 2 2 1 1 1 1 1 1 1 ...

Since each element in the list is the same length, you can convert it to a
data frame and use it as the population strata like so:

strata(asocial.gl) <- data.frame(other(asocial.gl))

When you do this, you can first set the population factor to be "basin" and
then use adegenet's built-in population-subsetting to extract the
Rhone_Valias population:

setPop(ascocial.gl) <- ~basin # assigns the "basin" column from the strata
to be the population factor (make sure you have the strata assigned first)

asocial.gl[pop = "Rhone_Valias"] # includes only the individuals in
Rhone_Valias

Hope that helps!
Zhian

Date: Thu, 25 Oct 2018 12:33:45 +0100
> From: Thibaut Jombart <thibautjombart at gmail.com>
> To: amaranta.fontcuberta at unil.ch
> Cc: "adegenet-forum at lists.r-forge.r-project.org"
>         <adegenet-forum at lists.r-forge.r-project.org>
> Subject: Re: [adegenet-forum] trouble accessing @other
> Message-ID:
>         <CANPRA+oJ_0Qa7zt2r=
> hEw5M3U9+EOr6_Z94faryW0q+vHZntzw at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi there,
>
> I think the NA in your logical vector may be the problem; can you try
> wrapping a 'which' around it?
>
> to_keep <- which(asocial.gl at other$basin=="Rhone_Valais")
> asocial.gl[to_keep,]
>
> Let us know if it works.
> Best
> Thibaut
>
> --
> Dr Thibaut Jombart
> Associate Professor in Outbreak Analytics, London School of Hygiene and
> Tropical Medicine
> Senior Lecturer in Genetic Analysis, Imperial College London
> President of RECON: repidemicsconsortium.org
> https://thibautjombart.netlify.com
> Twitter: @TeebzR
>
>
> On Thu, 25 Oct 2018 at 00:43, Amaranta Fontcuberta <
> amaranta.fontcuberta at unil.ch> wrote:
>
> > Hello,
> >
> > I want to subset part of the individuals of my genlight object according
> > to a variable stored in the @other slot. I get an error I don't
> understand.
> > I stored 3 categorical variables in the @other slot. It looks like that:
> > *> str(other(asocial.gl <http://asocial.gl>))*
> > List of 3
> >  $ basin : Factor w/ 3 levels "Rhine","Rhone_Valais",..: NA 2 NA 2 2 2 2
> 2
> > 2 2 ...
> >  $ Sgeno : Factor w/ 3 levels "mm","mp","pp": 1 2 3 1 1 1 1 1 1 1 ...
> >  $ Spheno: Factor w/ 2 levels "M","P": 1 2 2 1 1 1 1 1 1 1 ...
> >
> > When I try to subset my dataset, I get this error:
> > *> asocial.gl <http://asocial.gl>[asocial.gl at other
> $basin=="Rhone_Valais",]*
> > Error in .local(x, i, j, ..., drop = drop) :
> >   trying to get slot "n.loc" from an object of a basic class ("NULL")
> with
> > no slots
> >
> > The condition seems to work well, since when I call it alone, it outputs
> a
> > list of TRUE, FALSE that corresponds well to the individuals I want to
> > keep.
> > *> asocial.gl at other$basin=="Rhone_Valais"*
> >   [1]    NA FALSE    NA FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE
> >  TRUE  TRUE  TRUE
> >  [15]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE
> >  TRUE  TRUE  TRUE
> >  ...
> >
> > I use the same subseting command to select according to the @pop slot and
> > it works well.
> >
> >
> > Any help will be appreciated,
> >
> > Thanks a lot in advance,
> >
> > Amaranta.
> > ----------------------------------------------------------
> > Amaranta Fontcuberta, assistante dipl?m?e
> > Dept. ?cologie et ?volution
> > Universit? de Lausanne
> >
> > _______________________________________________
> > adegenet-forum mailing list
> > adegenet-forum at lists.r-forge.r-project.org
> >
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