[adegenet-forum] adegenet-forum Digest, Vol 127, Issue 2

Brian Simison bsimison at calacademy.org
Thu Apr 25 00:47:34 CEST 2019 

Thank you Zhian,
>From your description of dimnames, I was able to edit marker and genotype
labels until it worked.
And yes, I had the DAPC web running in the background.

FYI - Stacks2 <http://catchenlab.life.illinois.edu/stacks/>processes and
analyzes RADseq data. The 'populations
<http://catchenlab.life.illinois.edu/stacks/comp/populations.php>' script
does many things including exporting SNP data into various formats.



On Wed, Apr 24, 2019 at 3:21 AM Zhian Kamvar <
kamvarz at science.oregonstate.edu> wrote:

> The error you get is one of the more common generic R errors out there...
> and when it comes from a parsing function like this, it's hard to diagnose,
> but I'm going to guess that there is something going on with the names of
> the samples in your data (because of step 206). Old genetic data formats
> are _terrible_ for storing data because they force you to contort it in
> unnatural ways (not your fault at all, just how things are).
>
> The traceback you show is a bit strange... it shows a lot of noise from
> the dapcServer function, which shouldn't affect how read.genpop reads a
> file. Do you have dapcServer running?
>
> Can you give more detail? Things that are unclear:
>
> What is the Stacks2 'populations' script?
> What version of adegenet do you have?
> What version of R and RStudio are you running?
> Did you have to manually manipulate your data file to get it into genepop
> format?
>
>
>
> On Wed, Apr 24, 2019 at 11:00 AM <
> adegenet-forum-request at lists.r-forge.r-project.org> wrote:
>
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>>    1. length of 'dimnames' [1] not equal to array extent (Brian Simison)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 23 Apr 2019 12:03:35 -0700
>> From: Brian Simison <bsimison at calacademy.org>
>> To: adegenet-forum at lists.r-forge.r-project.org
>> Subject: [adegenet-forum] length of 'dimnames' [1] not equal to array
>>         extent
>> Message-ID:
>>         <CAM4LYpjCwSUHmn2SZUS_R5dzetc=
>> OFnoG4mKoNm8zoz8uZjh8g at mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> I have tried to convert various format output by Stacks2 'populations'
>> script with no success. I have tried both structure and genepop formats
>> and
>> continually get the cryptic error "length of 'dimnames' [1] not equal to
>> array extent"
>>
>> In Rstudio in Win10 I run:
>>  >Trach <- read.genepop("populations.gen")
>>
>>  Converting data from a Genepop .gen file to a genind object...
>>
>> File description:  2_52, 2_53, 2_74, 4_15, 4_18, 4_39, 4_84, 5_17, 5_35,
>> 5_61, 6_24, 6_49, 6_50, 6_88, ... (I deleted the middle of the file
>> description for space)
>> ... 45, 474683_54, 474839_33, 474839_38, 474839_56, 476311_31, 476311_59,
>> 476328_59, 477562_70, 477562_81, 479861_17
>> Warning: Error in <-: length of 'dimnames' [1] not equal to array extent
>>   206: rownames<-
>>   205: read.genepop
>>   204: import2genind
>>   203: <reactive:getData> [C:\Program
>> Files\R\R-3.5.1\library\adegenet\dapcServer/server.R#39]
>>   201: .func
>>   198: contextFunc
>>   197: env$runWith
>>   190: ctx$run
>>   189: self$.updateValue
>>   187: getData
>>   186: <reactive:getDapc> [C:\Program
>> Files\R\R-3.5.1\library\adegenet\dapcServer/server.R#222]
>>   184: .func
>>   181: contextFunc
>>   180: env$runWith
>>   173: ctx$run
>>   172: self$.updateValue
>>   170: getDapc
>>   169: renderPlot [C:\Program
>> Files\R\R-3.5.1\library\adegenet\dapcServer/server.R#248]
>>   167: func
>>   127: drawPlot
>>   113: <reactive:plotObj>
>>    97: drawReactive
>>    84: origRenderFunc
>>    83: output$scatterplot
>>     3: runApp
>>     2: .dapcServer
>>     1: adegenetServer
>> Warning: Error in <-: length of 'dimnames' [1] not equal to array extent
>>   101: <Anonymous>
>> Warning: Error in <-: length of 'dimnames' [1] not equal to array extent
>>   101: <Anonymous>
>> Warning: Error in <-: length of 'dimnames' [1] not equal to array extent
>>   101: <Anonymous>
>> Warning: Error in <-: length of 'dimnames' [1] not equal to array extent
>>   101: <Anonymous>
>>
>> I have searched for this error and have failed to understand what
>> "Dimnames" are.
>>
>> thank you in advance.
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> W. Brian Simison, Ph.D.
>> Curator & Director of Comparative Genomics
>> California Academy of Sciences
>> 55 Music Concourse Dr. SF, CA 94118
>> O:415.379.5297
>> M:415.310.1686
>> bsimison at calacademy.org
>> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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