[adegenet-forum] supplementary individuals

Jombart, Thibaut t.jombart at imperial.ac.uk
Thu Jan 16 15:24:05 CET 2014


after checking your data, this is a problem with your file. A comma is missing after one of your individual label (around line 2989, indiv HS11 I think). Once fixed all is fine.


From: adegenet-forum-bounces at lists.r-forge.r-project.org [adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Mark Coulson [Mark.Coulson at glasgow.ac.uk]
Sent: 15 January 2014 13:52
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] supplementary individuals

Dear all,

I am trying to bring in a genpop file of supplementary individuals to compare to my baseline file. Baseline file works just fine however when I try to bring in the supplementary file I get the following error message:

File description:  Title line:"all_farm_wild_SNP_data_35_markers"
Error in `rownames<-`(`*tmp*`, value = c("Eden_farm_01", "Eden_farm_02",  :
  length of 'dimnames' [1] not equal to array extent
In addition: Warning message:
In matrix(unlist(strsplit(vec.genot, "[[:space:]]+")), ncol = nloc,  :
  data length [105141] is not a sub-multiple or multiple of the number of rows [3005]

Not sure what exactly the above means, but I have figured out that the last 9 populations of the supplementary file appear to be causing the problem. If I remove them from the input file, the rest of the supplementary populations go in just fine.

Any thoughts? These last 9 populations are some of the most critical for my analysis!


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