[adegenet-forum] error in gstat.randtest

[Melanie Montes]

Thanks for the tip Thibaut!

In case anyone else ends up running into this error, it seems that it was
indeed the amount of missing data that was the problem. I tried keeping
different amounts, but found that any less that 98% missing (even 97.5%)
led to this error. This cut my dataset down from about 50 000 snps to 2800,
so you see how much was actually missing!

Thanks again,
Melanie



On Thu, Feb 9, 2017 at 11:53 AM, Thibaut Jombart <thibautjombart at gmail.com>
wrote:

> Hi Melanie,
>
> it's quite hard to tell without seeing the data, but yes, my suspicion is
> the same as yours, NAs are the culprits. Entirely non-typed loci are
> normally removed from genind objects during their construction, but it is
> still possible that for some groups in your data, some loci are entirely
> missing.
>
> Given how many SNPs you have, you can probably afford to remove loci with
> many missing data (just make sure you don't end up throwing too much away).
> propTyped(..., by = "loc") may be your friend here. Here's an example using
> microbov:
>
>
> > data(microbov)
>
> > propTyped(microbov, by = "loc")
>    INRA63     INRA5    ETH225    ILSTS5      HEL5      HEL1    INRA35
>  ETH152
> 0.9914773 0.9786932 0.9914773 0.9673295 0.9786932 0.9914773 0.9829545
> 0.9573864
>    INRA23     ETH10      HEL9    CSSM66    INRA32      ETH3    BM2113
>  BM1824
> 0.9644886 0.9943182 0.9701705 0.9886364 0.9687500 0.9829545 0.9914773
> 0.9900568
>     HEL13    INRA37    BM1818    ILSTS6      MM12    CSRM60    ETH185
>  HAUT24
> 0.9772727 0.9815341 0.9588068 0.9446023 0.9744318 0.9730114 0.9275568
> 0.9872159
>    HAUT27   TGLA227   TGLA126   TGLA122    TGLA53    SPS115
> 0.9914773 0.9914773 0.9914773 0.9914773 0.9531250 0.9701705
>
> > to_keep <-   propTyped(microbov, by = "loc") > .99  # i.e. less 1%
> missing data
>
> > to_keep
>  INRA63   INRA5  ETH225  ILSTS5    HEL5    HEL1  INRA35  ETH152  INRA23
> ETH10
>    TRUE   FALSE    TRUE   FALSE   FALSE    TRUE   FALSE   FALSE   FALSE
>  TRUE
>    HEL9  CSSM66  INRA32    ETH3  BM2113  BM1824   HEL13  INRA37  BM1818
>  ILSTS6
>   FALSE   FALSE   FALSE   FALSE    TRUE    TRUE   FALSE   FALSE   FALSE
> FALSE
>    MM12  CSRM60  ETH185  HAUT24  HAUT27 TGLA227 TGLA126 TGLA122  TGLA53
>  SPS115
>   FALSE   FALSE   FALSE   FALSE    TRUE    TRUE    TRUE    TRUE   FALSE
> FALSE
>
> > x <- microbov[loc = to_keep]
>
> > nLoc(x)
> [1] 10
>
> > nLoc(microbov)
> [1] 30
>
>
> This is just an illustration - this dataset actually has little in terms
> of missing data. In your case you probably want to play with the threshold
> (99% non-NA is likely an overkill).
>
> Cheers
> Thibaut
>
>
>
> --
> Dr Thibaut Jombart
> Lecturer, Department of Infectious Disease Epidemiology, Imperial College
> London
> Head of RECON: repidemicsconsortium.org
> sites.google.com/site/thibautjombart/
> github.com/thibautjombart
> Twitter: @TeebzR <http://twitter.com/TeebzR>
> +44(0)20 7594 3658 <+44%2020%207594%203658>
>
> On 8 February 2017 at 11:14, Melanie Montes <melaniesmontes at gmail.com>
> wrote:
>
>> Hello all,
>> I recently finished running fstat on my dataset of about 50 000 snps / 56
>> individuals, and successfully got f-statistics in return. However, when I
>> tried to run gstat.randtest to see if the structure was significant:
>>
>> fstat.sig <-gstat.randtest(nr2014, nsim=1000)
>> ...I got 50+ warnings like this:
>>
>> 50: In max(y, na.rm = TRUE) : no non-missing arguments to max; returning
>> -Inf
>>
>> and my results file looked like this:
>>
>> > fstat.sig
>>
>> Monte-Carlo test
>>
>> Call: gstat.randtest(x = nr2014, nsim = 1000)
>>
>> Observation: 0
>>
>> Based on 1000 replicates
>>
>> Simulated p-value: 1
>>
>>
>> which leads me to suspect that it did not work. Does this have something
>> to do with the missing data in my dataset? Sorry if this is a naive
>> question, I am an R novice.
>>
>> Thanks for your time and the awesome package, I've been using it a lot!
>>
>> Sincerely,
>> Melanie
>>
>> _______________________________________________
>> adegenet-forum mailing list
>> adegenet-forum at lists.r-forge.r-project.org
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo
>> /adegenet-forum
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.r-forge.r-project.org/pipermail/adegenet-forum/attachments/20170223/c872f341/attachment.html>