[adegenet-forum] adegenet-forum Digest, Vol 152, Issue 1

[Zhian Kamvar]

Sorry for the late reply. You should use

ploidy(SNPs_Ploidy) <- c(4, 2, 4, 4, 4, 4, 2, 4, 4, 4)

The error you were getting was due to the fact that you were passing a
single character to the ploidy function. It expects a numeric or integer
vector.

On Tue, Feb 7, 2023 at 3:00 AM <
adegenet-forum-request at lists.r-forge.r-project.org> wrote:

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>    1. Changing Ploidy (Swati...)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 6 Feb 2023 13:06:12 +0100
> From: "Swati..." <swatipuraanik at gmail.com>
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] Changing Ploidy
> Message-ID:
>         <CAD-12nFrXh1F7DdP=
> b34T0q5q8QqLToyLaANQOQ2W591HjLMmQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,
>
> I have a Genlight object as below:
>
> > SNPs_Ploidy  /// GENLIGHT OBJECT /////////
>
>  // 78 genotypes,  8,368 binary SNPs, size: 33.2 Mb
>  23935 (3.67 %) missing data
>
>  // Basic content
>    @gen: list of 78 SNPbin
>    *@ploidy: ploidy of each individual  (range: 2-2)*
>
>  // Optional content
>    @ind.names:  78 individual labels
>    @loc.names:  8368 locus labels
>    @loc.all:  8368 alleles
>    @position: integer storing positions of the SNPs
>    @pop: population of each individual (group size range: 3-50)
>    @other: a list containing: loc.metrics  ind.metrics
> loc.metrics.flags  verbose  history
>
>
> As you can see @ploidy: ploidy of each individual (range: 2-2). However the
> 78 individuals in my dataset have all different ploidies ranging from 2X to
> 6X. I tried using these commands:
>
> > head(ploidy(SNPs_Ploidy), 10)
>
>   Ac-3 Ac-359  Ac-25  Ac-75 Ac-182 Ac-210 Ac-272 Ac-317 Ac-333 Ac-344
>
>      2      2      2      2      2      2      2      2      2      2
>
>
>
> > ploidy(SNPs_Ploidy) <- paste("4", "2", "4", "4", "4", "4", "2", "4", "4",
> "4", sep=" ")
>
>
> But I get this error message:
>
> Error in `ploidy<-`(`*tmp*`, value = "4 2 4 4 4 4 2 4 4 4") :
>   (converted from warning) NAs introduced by coercion
>
> Is it possible to change the ploidy and what could be the appropriate
> commands?
>
> Best Regards
> Swati
> --------------------------------------------------------------- _
> ---------- ----------------------
> *SWATI PURANIK ,  Ph.D.,  MSCA Fellow*
> Junior Researcher
> Global Change Research Institute (CzechGlobe), Czech Academy of Sciences
> Bělidla 986/4a, 603 00 Brno; Czech Republic
> E-mail: s <manoj_prasad at nipgr.ac.in>watipuraanik at gmail.com
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