[adegenet-forum] Problem converting structure file to genind (length of 'dimnames' [2] not equal to array extent)

[Jombart, Thibaut]

Hi Charlotte,

thanks for a detailed report.

STRUCTURE files are a bit of a pain because of all the possible options, so in general if you can get them in a different format (e.g. GENETIX, Fstat) it will make your life easier.

Here, your instruction seems okay given the sample of the file, but the file itself seems wrong. STRUCTURE's doc suggests you should remove 'Ind' and 'Pop' from the first line.
http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/structure_doc.pdf

It works on the sample provided.

Was this file generated by STRUCTURE directly?

If the STRUCTURE standards have changed, please fill in an issue and we'll adapt read.structure:
https://github.com/thibautjombart/adegenet/issues

Best
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 Charlotte Hurry [charlotte.hurry at griffithuni.edu.au]
Sent: 24 July 2015 05:08
To: adegenet-forum at lists.r-forge.r-project.org
Subject: [adegenet-forum] Problem converting structure file to genind (length of 'dimnames' [2] not equal to array extent)

Hello
I have been trying to convert my structure file to a genind object but I am having some issues.  I am getting this error and I can't find an appropriate fix.  I have looked through forum history and found a similar issue but the fix suggested didn't work for me.

my file looks like this:
Ind    Pop    tb109    tb117    tb129    tb130    tb136    tb187    tb188
GM4_283    1    118    108    132    125    122    168    159
GM4_283    1    120    112    138    129    122    176    168
GM336    1    114    112    128    123    124    168    0
GM336    1    116    112    136    123    128    176    0
GM337    1    0    110    126    123    126    168    159
GM337    1    0    112    126    123    126    176    174
E276    2    118    108    0    0    122    166    165
E276    2    118    112    0    0    122    176    190
E277    2    116    108    126    119    124    168    159
E277    2    118    112    138    129    128    176    174
E278    2    114    108    124    121    122    168    162
E278    2    114    112    126    125    128    176    180

I used the script
> tems<-read.structure("TBtest1.str",row.marknames=1,onerowperind=FALSE, n.ind=190, n.loc=7, col.lab=1, col.pop=2, ask=TRUE)

Which brings up the following message, and I press RETURN:
 Which other optional columns should be read (press 'return' when done)? 1:

 Converting data from a STRUCTURE .stru file to a genind object...

Then get this error:

Error in `colnames<-`(`*tmp*`, value = c("Ind", "Pop", "tb109", "tb117",  :
  length of 'dimnames' [2] not equal to array extent

Has anybody got a fix to get my original STRUCTURE file to work as a Genind object.?

As an aside, on the forum I found a work around under the title "Trouble converting to genid object", which converts a read.table document into genind which I followed and I got this error:
Warning message:
In .local(.Object, ...) : NAs introduced by coercion
and this file:
> head(as.matrix(obj1))
    V1 V2  V3  V4  V5  V6  V7  V8  V9
001 NA NA  NA  NA  NA  NA  NA  NA  NA
002 NA  1 118 108 132 125 122 168 159
003 NA  1 120 112 138 129 122 176 168
004 NA  1 114 112 128 123 124 168   0
005 NA  1 116 112 136 123 128 176   0
006 NA  1   0 110 126 123 126 168 159

So i would like a different solution to my problem if possible.
Many thanks
Charlotte


Charlotte

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