[adegenet-forum] input file problem!

[Jombart, Thibaut]

Dear Avik,

The problem is not a but in df2genind as I first feared, but an issue in your data. Line 59, loci 2 reads:
353/353/345345

The missing separator creates the problem. I thought about issuing a warning for that kind of typo, but I don't think it would be a good deal in terms of computational time.

All the best

Thibaut

________________________________
From: adegenet-forum-bounces at r-forge.wu-wien.ac.at [adegenet-forum-bounces at r-forge.wu-wien.ac.at] on behalf of AVIK RAY [avik.ray.kol at gmail.com]
Sent: 09 June 2011 09:54
To: adegenet-forum at r-forge.wu-wien.ac.at
Subject: [adegenet-forum] input file problem!

Hi All

I am trying to do PCA with tetraploid data;  204 individuals, 7 loci, with some missing data, and the command goes like this

..........
> obj<-read.table("infileAll.txt")
> obj
…………….
…………….
> dat<-data.frame(obj)
> dat
…………….
…………….
> x<-df2genind(dat, sep="/", ploidy=4)
Error in data.frame(c("366", "366", "366", "378"), c("366", "366", "366",  :
  arguments imply differing number of rows: 4, 1, 3
In addition: Warning message:
In df2genind(dat, sep = "/", ploidy = 4) :
  entirely non-type individual(s) deleted
......................

so, do not know what is going wrong in it! I guess there is some problem with the input file so it's not accepted in R; earlier with small dataset it worked fine;
please suggest a solution
Thanks
AVIK
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