[adegenet-forum] adegenet-forum Digest, Vol 135, Issue 1

[Zhian Kamvar]

Hello,

You can import your data with read.csv() and then use `as.genlight()` to
convert the allele counts into a genlight object.
Hope that helps.

Best, Zhian

On Sat, Feb 1, 2020 at 11:00 AM <
adegenet-forum-request at lists.r-forge.r-project.org> wrote:

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> Today's Topics:
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>    1. potato dosage SNP (weiya xue)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 31 Jan 2020 12:04:18 -0500
> From: weiya xue <xueweiya at gmail.com>
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] potato dosage SNP
> Message-ID:
>         <
> CAK59EjBEo0sko7MY2AQvH+L+UOrTRAxxpMuDU_twsGbLvOz1Zg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Dr. Zhian N. Kamvar,
>
> I am potato postdoc researcher at Pennsylvania  state university. I
> have a question when I use  adegenet R package for DAPC analysis .
>
> My SNP data were coded as dosage 0,1,2,3,4  in csv file(sample data
> attached). When I used read.csv to read this data into R, which
> function should I use to convert it into adegent format for next
> steps?
>
>
>
> And when I use  read.structure,  I always get the below information.
>
>
>
> Error in mat[, (ncol(mat) - p + 1):ncol(mat)] :
>
>   only 0's may be mixed with negative subscripts
>
>
>
> Thanks a lot,
>
> Weiya Xue
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