[adegenet-forum] adegenet-forum Digest, Vol 132, Issue 2

[Zhian Kamvar]

Hello,

The dapc() function can take a matrix as input. Just make sure that you
have it oriented so that the columns represent your CNV events.

Best,
Zhian

On Mon, Nov 18, 2019 at 10:27 AM <
adegenet-forum-request at lists.r-forge.r-project.org> wrote:

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>    1. scCNV input to DAPC (Kimberly Ann McLaughlin)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 18 Nov 2019 00:25:16 +0000
> From: Kimberly Ann McLaughlin <kimberly.mclaughlin at northwestern.edu>
> To: "adegenet-forum at lists.r-forge.r-project.org"
>         <adegenet-forum at lists.r-forge.r-project.org>
> Subject: [adegenet-forum] scCNV input to DAPC
> Message-ID: <1574036716274.57987 at northwestern.edu>
> Content-Type: text/plain; charset="iso-8859-1"
>
> ?
>
> I'm trying to cluster scCNV data from 10X Genomics by clone using
> Adegenet's DAPC. I'm following the method in this paper and the R code to
> generate a CNV mutation matrix is provided in the supplement. However, it
> isn't clear to me how to input this matrix into Adegenet. Does anyone have
> any advice on how to do this or any alternatives to the matrix to use as
> input?
>
>
>
> https://www.biorxiv.org/content/biorxiv/early/2019/09/05/757211.full.pdf
>
>
> https://www.biorxiv.org/content/10.1101/757211v1.supplementary-material
>
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