[adegenet-forum] read.PLINK error message

[Zhian Kamvar]

Hi Ashley,

I suspect that the PLINK format has changed somewhat since this function
was initially written (before 2014). If you have a VCF file, it would be
better to use the {vcfR} package to convert to genlight or genclone (or
even genind).

To do so, you can use:
vcf <- vcfR::read.vcfR("/path/to/my.vcf")

with

vcfR::vcfR2genlight(vcf) to return a genlight object

or

vcfR::vcfR2genind(vcf, return.alleles = TRUE) to return a genind object

I hope that helps. Sorry for the late reply.

Best,
Zhian

> Date: Mon, 4 Dec 2023 19:40:39 -0800
> From: Ashley A Dickinson <Ashley.Dickinson at humboldt.edu>
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] read.PLINK error message
> Message-ID:
>         <CAGM_n_=
> R5oWBJSA__aKGveZyyOn96qHxKEj8j_Q7L9ES8nv0rg at mail.gmail.com>
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>
> Hello,
>
> I am trying to use adagenet (v.2.1.10) to do DAPC, but I am receiving an
> error message I can't figure out. I used PLINK2 to convert a vcf file to a
> .raw file for SNP data obtained on 78 individuals using RADseq. I then
> tried to use the read.PLINK function to import into genlight objects
>
> > read.PLINK("myfile.raw", map.file = "myfile.map")
>
> Reading PLINK raw format into a genlight object...
> Reading loci information...
> Reading and converting genotypes...
> .Error in read.PLINK("myfile.raw", map.file = "myfile.map") :
>   some individuals do not have -5 SNPs.
>
>
> I have tried again with multiple different vcf output files that I had
> created with different parameters and filtering steps just to make sure
> that it wasn't that one file, but I get the same error each time. The data
> set has >8000 SNPs within 730 loci.
>
> Any ideas or recommendations are appreciated!
>
> -Ashley
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