[adegenet-forum] Error with read.PLINK and extract.PLINKmap

Jombart, Thibaut t.jombart at imperial.ac.uk
Fri Oct 9 12:49:12 CEST 2015

Dear Kristin,

it is hard to figure out what is happening from the error message.

Could you post an "Issue" on github with a reproducible example (code + data)?



From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Kristin Alligood [kristin.alligood at gmail.com]
Sent: 09 October 2015 03:13
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Error with read.PLINK and extract.PLINKmap

I am having trouble importing my data into adegenet using the read.PLINK command.  I have converted my data into a plink.raw file using --recodeA, but am getting an error when I try to load my data:

MIplink <- read.PLINK("plink.raw")
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),  :
  1 function calls resulted in an error

I am also having trouble using the extract.PLINKmap command and get this error:

Pmap <- extract.PLINKmap("batch_1.plink.map")
Error in factor(txt[ord, 1]) : object 'ord' not found
In addition: Warning message:
In matrix(txt, ncol = 4, byrow = TRUE) :
  data length [3997] is not a sub-multiple or multiple of the number of rows [1000]

In looking through the archives, I have seen that other people have encountered similar problems, but I couldn't find a posted solution.  The problem with read.PLINK was posted in the July 2014 archives subject read.PLINK error, and the problem with extract.PLINKmap was posted in the January 2013 archives subject extract.PLINKmap.

My apologies if I'm being redundant or missing the solutions somehow. Any feedback would be great!

I'm using adegenet version 2.0.1
>packageDescription("adegenet", field="Version")
>[1] "2.0.1"

Thanks so much.

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