[adegenet-forum] adegenet-forum Digest, Vol 126, Issue 1

[Zhian Kamvar]

Hi Samuel,

The tab function simply gives back a matrix of allele counts (for a
genlight object). It won't replace the values IN the genlight object (since
R is side-effect free).

Because of the way a genlight object works, you can't replace the values
with the average counts of alleles, so what you might want to do is to use
`tab()` to get the allele matrix with missing replaced with the mean value
and then use `celing()` on that matrix to transform the average values to
the nearest allele copy number (note: you could also use `round()`, but
this will always round to the nearest even digit). From there, you can
convert back to a genlight with the missing values replaced.

On Mon, Mar 4, 2019 at 11:00 AM <
adegenet-forum-request at lists.r-forge.r-project.org> wrote:

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>    1. Replacing NAs in genlight object (Samuel Weaver)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Sun, 3 Mar 2019 12:53:16 -0600
> From: Samuel Weaver <weave271 at umn.edu>
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] Replacing NAs in genlight object
> Message-ID:
>         <CAAeinLC0PVGsy7wrXdSrJLv7wDogqdiXvF+8FH3SPC=
> enha-qA at mail.gmail.com>
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> I'm trying to change NAs in my dataset to the mean allele frequency to run
> various PopGen analyses through adegenet, but have been having trouble.
> Commands start below.
>
> Data<-vcfR2genlight(MyVcf)
> Data
> /// GENLIGHT OBJECT /////////
>
>  // 11 genotypes,  5,467 binary SNPs, size: 877.8 Kb
>  7647 (12.72 %) missing data
>
>  // Basic content
>    @gen: list of 11 SNPbin
>
>  // Optional content
>    @ind.names:  11 individual labels
>    @loc.names:  5467 locus labels
>    @chromosome: factor storing chromosomes of the SNPs
>    @position: integer storing positions of the SNPs
>    @other: a list containing: elements without names
>
> I then try to run the command listed in the tutorial and elsewhere on the
> forum, which is as follows:
>
> tab(Data, NA.method="mean").
>
> This, however, does nothing to replace the NA values in the original "Data"
> genlight object. I've looked for hours on how to do this with no avail, so
> any help would be greatly appreciated.
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