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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Charlotte,
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thanks for a detailed report. <br>
<br>
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.<br>
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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.<br>
http://pritchardlab.stanford.edu/structure_software/release_versions/v2.3.4/structure_doc.pdf<br>
<br>
It works on the sample provided.<br>
<br>
Was this file generated by STRUCTURE directly?<br>
<br>
If the STRUCTURE standards have changed, please fill in an issue and we'll adapt read.structure:<br>
<a href="https://github.com/thibautjombart/adegenet/issues" target="_blank">https://github.com/thibautjombart/adegenet/issues</a><br>
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Best<br>
Thibaut <br>
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<div style="direction: ltr;" id="divRpF60880"><font face="Tahoma" color="#000000" size="2"><b>From:</b> adegenet-forum-bounces@lists.r-forge.r-project.org [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of Charlotte Hurry [charlotte.hurry@griffithuni.edu.au]<br>
<b>Sent:</b> 24 July 2015 05:08<br>
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> [adegenet-forum] Problem converting structure file to genind (length of 'dimnames' [2] not equal to array extent)<br>
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<h1><span style="font-weight:normal">Hello</span><br>
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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.<br>
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my file looks like this:<br>
Ind Pop tb109 tb117 tb129 tb130 tb136 tb187 tb188<br>
GM4_283 1 118 108 132 125 122 168 159<br>
GM4_283 1 120 112 138 129 122 176 168<br>
GM336 1 114 112 128 123 124 168 0<br>
GM336 1 116 112 136 123 128 176 0<br>
GM337 1 0 110 126 123 126 168 159<br>
GM337 1 0 112 126 123 126 176 174<br>
E276 2 118 108 0 0 122 166 165<br>
E276 2 118 112 0 0 122 176 190<br>
E277 2 116 108 126 119 124 168 159<br>
E277 2 118 112 138 129 128 176 174<br>
E278 2 114 108 124 121 122 168 162<br>
E278 2 114 112 126 125 128 176 180<br>
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I used the script<br>
<b>> tems<-read.structure("TBtest1.str",row.marknames=1,onerowperind=FALSE, n.ind=190, n.loc=7, col.lab=1, col.pop=2, ask=TRUE)</b><br>
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Which brings up the following message, and I press RETURN: <br>
<b> Which other optional columns should be read (press 'return' when done)? 1: <br>
<br>
Converting data from a STRUCTURE .stru file to a genind object... </b><br>
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Then get this error:<br>
<br>
<b>Error in `colnames<-`(`*tmp*`, value = c("Ind", "Pop", "tb109", "tb117", : <br>
length of 'dimnames' [2] not equal to array extent<br>
</b><br>
Has anybody got a fix to get my original STRUCTURE file to work as a Genind object.?<br>
<br>
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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:<br>
Warning message:<br>
In .local(.Object, ...) : NAs introduced by coercion <br>
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and this file:<br>
> head(as.matrix(obj1))<br>
V1 V2 V3 V4 V5 V6 V7 V8 V9<br>
001 NA NA NA NA NA NA NA NA NA<br>
002 NA 1 118 108 132 125 122 168 159<br>
003 NA 1 120 112 138 129 122 176 168<br>
004 NA 1 114 112 128 123 124 168 0<br>
005 NA 1 116 112 136 123 128 176 0<br>
006 NA 1 0 110 126 123 126 168 159<br>
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So i would like a different solution to my problem if possible.<br>
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Many thanks<br>
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Charlotte<br>
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<div dir="ltr"><span>Charlotte<br>
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