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

Kristin Alligood kristin.alligood at gmail.com
Fri Oct 9 04:13:34 CEST 2015

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
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
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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