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<div style="direction: ltr;font-family: Tahoma;color: #000000;font-size: 10pt;">Hi Vikram,
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you are right. This is one of the many reasons behind the changes in adegenet 2.0-0, in which we drop the generic names altogether. We plan to release this new version over the month to come. Meanwhile, it can be installed easily from github:<br>
https://github.com/thibautjombart/adegenet<br>
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Cheers<br>
Thibaut<br>
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==============================<br>
Dr Thibaut Jombart<br>
MRC Centre for Outbreak Analysis and Modelling<br>
Department of Infectious Disease Epidemiology<br>
Imperial College - School of Public Health<br>
Norfolk Place, London W2 1PG, UK<br>
Tel. : 0044 (0)20 7594 3658<br>
http://sites.google.com/site/thibautjombart/<br>
http://sites.google.com/site/therepiproject/<br>
http://adegenet.r-forge.r-project.org/<br>
Twitter: @thibautjombart<br>
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<div style="direction: ltr;" id="divRpF839368"><font face="Tahoma" size="2" color="#000000"><b>From:</b> adegenet-forum-bounces@lists.r-forge.r-project.org [adegenet-forum-bounces@lists.r-forge.r-project.org] on behalf of Vikram Chhatre [crypticlineage@gmail.com]<br>
<b>Sent:</b> 08 April 2015 21:45<br>
<b>To:</b> adegenet-forum@lists.r-forge.r-project.org<br>
<b>Subject:</b> [adegenet-forum] Keeping track of truenames<br>
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<div dir="ltr">When importing from Structure format, if the data contains entirely non-type markers, the import2genind function will remove such sites. The remaining sites, as it appears, are then sequentially named from L001 to L00n. Thus the identity of
loci is lost.
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<div>But it is possible to restore the original site names i.e. truenames in either genind or genpop objects.</div>
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<div>mygenind_tn <- truenames(mygenind)</div>
<div>mygenpop_tn <- truenames(mygenpop)</div>
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<div>At least that's how I am interpreting this. Please correct me if I am wrong.</div>
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<div>A couple of observations, based on this:</div>
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<div>1. After you apply truenames to the genpop object, contents of mygenpop$tab == mygenpop_tn. In other words, mygenpop_tn$table will not yield anything. Instead mygenpop_tn itself yields the allele count table.</div>
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<div>2. If you apply truenames to a genind object, it is no longer recognized as a genind object.</div>
<div>mygenpop_tn2 <- genind2genpop(mygenind_tn)</div>
<div>Error in genind2genpop(mygenind_tn): x is not a valid genind object.</div>
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<div>3. Likewise, mygenpop_tn isn't a valid genpop object either anymore. For example:</div>
<div>myfreq <- makefreq(mygenpop_tn)</div>
<div>Error in makefreq(mygenpop_tn): x is not a valid genpop object.</div>
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<div>So my question is how can I restore truenames for sites and samples without breaking the genind and genpop objects?</div>
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<div>Thanks</div>
<div>Vikram</div>
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