[adegenet-forum] Keeping track of truenames

[Vikram Chhatre]

As Zhian pointed out on github (
https://github.com/thibautjombart/adegenet/issues/46), this isn't a bug.
One just needs to tell adegenet what row contains marker names.

mygenind <- import2genind('infile.str', onerowperind=F, row.marknames=1,
n.ind=5, n.loc=10, col.lab=1, col.pop=2, ask=F)

Now the genind object contains actual locus names, not generic ones.

Thanks.
Vikram

On Tue, Apr 14, 2015 at 11:49 AM, Vikram Chhatre <crypticlineage at gmail.com>
wrote:

> Will do, thank you.
>
> In the meantime, is there a quick way to get a list of markers that were
> deemed 'entirely nontype' by adegenet?
>
> Thanks
> Vikram
>
> On Tue, Apr 14, 2015 at 11:34 AM, Jombart, Thibaut <
> t.jombart at imperial.ac.uk> wrote:
>
>>  Hi there,
>>
>> can you please post this as an issue on github, including a reproducible
>> example of the problem?
>> https://github.com/thibautjombart/adegenet/issues
>>
>> Cheers
>> Thibaut
>>
>>    ------------------------------
>> *From:* Vikram Chhatre [crypticlineage at gmail.com]
>> *Sent:* 14 April 2015 16:22
>> *To:* Jombart, Thibaut; adegenet-forum at lists.r-forge.r-project.org
>> *Subject:* Re: [adegenet-forum] Keeping track of truenames
>>
>>   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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