[adegenet-forum] Keeping track of truenames

[Vikram Chhatre]

Hi Thibaut and others,

After installing Adegenet 2.0, I am still seeing the generic locus and
individual names.  I am converting vcf files to structure format before
importing it as a genind object.  The structure file have actual locus and
individual names which are lost in the genind object.

Although, different from 1.4, the new version appears to assign generic
names *before* deleting entirely nontype markers, thus, the sequence of
names (though generic) is maintained.  Still linking these generic names
back to their actual names isn't a piece of cake (I wonder if this can be
done within R?)

Starting loci: M45, S29, P10, K46
Genind loci: L01, L02, L03, L04

Allele frequency table contains only two loci: L02, L04 because L01 and L03
are monomorphic.

V

On Thu, Apr 9, 2015 at 5:27 AM, Jombart, Thibaut <t.jombart at imperial.ac.uk>
wrote:

>  Hi Vikram,
>
> 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:
> https://github.com/thibautjombart/adegenet
>
> Cheers
> Thibaut
>
> ==============================
> Dr Thibaut Jombart
> MRC Centre for Outbreak Analysis and Modelling
> Department of Infectious Disease Epidemiology
> Imperial College - School of Public Health
> Norfolk Place, London W2 1PG, UK
> Tel. : 0044 (0)20 7594 3658
> http://sites.google.com/site/thibautjombart/
> http://sites.google.com/site/therepiproject/
> http://adegenet.r-forge.r-project.org/
> Twitter: @thibautjombart
>
>
>    ------------------------------
> *From:* adegenet-forum-bounces at lists.r-forge.r-project.org [
> adegenet-forum-bounces at lists.r-forge.r-project.org] on behalf of Vikram
> Chhatre [crypticlineage at gmail.com]
> *Sent:* 08 April 2015 21:45
> *To:* adegenet-forum at lists.r-forge.r-project.org
> *Subject:* [adegenet-forum] Keeping track of truenames
>
>   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.
>
>  But it is possible to restore the original site names i.e. truenames in
> either genind or genpop objects.
>
>  mygenind_tn <- truenames(mygenind)
> mygenpop_tn <- truenames(mygenpop)
>
>  At least that's how I am interpreting this. Please correct me if I am
> wrong.
>
>  A couple of observations, based on this:
>
>  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.
>
>  2. If you apply truenames to a genind object, it is no longer recognized
> as a genind object.
> mygenpop_tn2 <- genind2genpop(mygenind_tn)
> Error in genind2genpop(mygenind_tn): x is not a valid genind object.
>
>  3. Likewise, mygenpop_tn isn't a valid genpop object either anymore.
> For example:
> myfreq <- makefreq(mygenpop_tn)
> Error in makefreq(mygenpop_tn): x is not a valid genpop object.
>
>  So my question is how can I restore truenames for sites and samples
> without breaking the genind and genpop objects?
>
>  Thanks
> Vikram
>
>
>
>
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