[adegenet-forum] read.PLINK error

[Jombart, Thibaut]

Hi there, 

I confess I never use vcftools so I'm not sure what it's been doing to your data, but it looks like the format might have been altered. 

I Cc Emmanuel Paradis (ape, pegas, ...) who I think might have been developing something for this kind of data recently.

Best
Thibaut




________________________________________
From: ADAM PETER CARDILINI [apcar at deakin.edu.au]
Sent: 08 June 2014 23:24
To: Jombart, Thibaut
Cc: adegenet-forum at lists.r-forge.r-project.org
Subject: Re: read.PLINK error

G'day Thibaut,

Sorry I should have included that in the original email.

The code I use to read the data was:

dat <- read.PLINK('myfiltered_plinkconvertedfile.raw', map.file = 'myfiltered_plinkconvertedfile.map')

This command line worked on the unfiltered data files, just not the ones I got after filtering in vcftools.

Cheers,
Adam

Sent from my iPad

> On 9 Jun 2014, at 3:42 am, "Jombart, Thibaut" <t.jombart at imperial.ac.uk> wrote:
>
>
> Hello,
>
> what command line did you use to read the data?
>
> Cheers
> Thibaut
> ________________________________________
> From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of ADAM PETER CARDILINI [apcar at deakin.edu.au]
> Sent: 06 June 2014 03:44
> To: adegenet-forum at lists.r-forge.r-project.org
> Subject: [adegenet-forum] read.PLINK error
>
> G’day Everyone,
>
> I have recently produced a .vcf file for a set of SNPs obtained using Genotype-by-sequencing. The .vcf file is the final output from the TASSEL pipeline which takes in fastq sequence files. I converted my .vcf file to a .ped and .map files using vcftools and then converted the .ped file to .raw so that I could load it into R using ’adegenet’ function ‘read.PLINK’. The linux vcftools and plink code was as follows:
>
> vcftools --vcf myfile.vcf --out myfile.plink --plink
> plink --file myfile.plink --out myfile.plink --recodeA
>
> I successfully loaded my unaltered file into R using ‘adegenet’, however it has way many SNPs that I am not interested in (because it has only been sequenced for a couple of individuals) so I thought I would filter my .vcf snp file using vcftools. I filtered my original file so that only SNPs that were sequenced from >90% of samples remained. This significantly reduced the number of SNPs I had and produced a new .vcf file. I then converted this file to .ped and .map, and then .ped to .raw so I could bring it into R and have a quick look.
>
> When I tried to import the new, filtered .raw file using ‘read.PLINK’ I got the following error:
>
>
> Reading PLINK raw format into a genlight object...
>
> Reading loci information...
>
> Reading and converting genotypes...
> .Error in (function (classes, fdef, mtable)  :
>  unable to find an inherited method for function ‘nLoc’ for signature ‘"try-error"’
> In addition: Warning message:
> In mclapply(txt, function(e) new("SNPbin", snp = e, ploidy = 2),  :
>  9 function calls resulted in an error
>
>
>
> It seems as if something has gone wrong when I have produced the new .vcf file during filtering. I was wondering if anyone might know what I have done wrong, what these error messages mean and whether there is a fix I can try?
>
> Thanks in advance for your time and help, I appreciate it.
>
> Kind regards,
>
> Adam Cardilini
> PhD Candidate
> Schools of Life and Environmental Sciences,
> Deakin University, 75 Pigdons Rd,
> Waurn Ponds, Vic, Australia, 3217
> Mob: 0431 566 340
> Email: apcar at deakin.edu.au
>