[adegenet-forum] How can I filter out loci out of HWE from a genind object?

[Vikram Chhatre]

Indeed.  I was using the github version of adegenet 2.0.0.  After
reinstalling the package directly, method# 1 is now working.

Thanks
V

On Tue, Jul 28, 2015 at 11:08 AM, Jombart, Thibaut <t.jombart at imperial.ac.uk
> wrote:

>  Hmmm... weird.
>
> Method #2 will not work, but #1 should. Can you try this and tell us what
> you get:
>
> library(adegenet)
> data(nancycats)
> nancycats[loc=-1]
>
> One possibility is that your adegenet 2.0.0 was the old from github. So
> maybe trying again after
>
> install.packages("adegenet")
>
> would be worth a try?
> Cheers
> Thibaut
>
>    ------------------------------
> *From:* Vikram Chhatre [crypticlineage at gmail.com]
> *Sent:* 28 July 2015 15:52
> *To:* adegenet-forum at lists.r-forge.r-project.org
> *Cc:* Jombart, Thibaut
> *Subject:* Re: [adegenet-forum] How can I filter out loci out of HWE from
> a genind object?
>
>   Hi Thibaut,
>
>  This does not seem to work. Perhaps I am doing something wrong.  Here is
> an example:
>
>  head(locNames(mygenind))
> [1] "loc_121" "loc_229" "loc_472" "loc510" "loc688"
>
>  ## Method 1
> rmloci <- c(1,3)
> mygenind2 <- mygenind[loci=-rmloci]
> Warning message:
> In .local(x, i, j, ..., drop = drop) :
>   the following specified loci do not exist: -1the following specified
> loci do not exist: -3
>
>  ## Method 2
> rmloci2 <- c("loc_121","loc_472")
> mygenind2 <- mygenind[loci=-rmloci2]
> Error in -rmloci : invalid argument to unary operator
>
>  sessionInfo()
> adegenet_2.0.0
> ade4_1.6-2
> R 3.1.2
>
>  Thanks
> V
>
>
>
> On Tue, Jul 28, 2015 at 10:31 AM, Jombart, Thibaut <
> t.jombart at imperial.ac.uk> wrote:
>
>>  Hi there,
>>
>> this is easy to do since adegenet 2.0.0. You can use x[loc=...] where ...
>> is any usual subsetting, which will be matched against locNames(x). You can
>> use it to retain relevant loci, or discard the unwanted ones.
>>
>> For instance:
>>
>> > library(adegenet)
>> Loading required package: ade4
>>
>>    /// adegenet 2.0.0 is loaded ////////////
>>
>>    > overview: '?adegenet'
>>    > tutorials/doc/questions: 'adegenetWeb()'
>>    > bug reports/feature resquests: adegenetIssues()
>>
>>
>> > data(nancycats)
>>
>>
>> *> locNames(nancycats) [1] "fca8"  "fca23" "fca43" "fca45" "fca77"
>> "fca78" "fca90" "fca96" "fca37" *
>> *## removing loci 2, 4 and 5*
>> > toRemove= c(2,4,5)
>> > x=nancycats[loc=-toRemove]
>> > x
>> /// GENIND OBJECT /////////
>>
>>  // 237 individuals; 6 loci; 76 alleles; size: 102.9 Kb
>>
>>  // Basic content
>>    @tab:  237 x 76 matrix of allele counts
>>    @loc.n.all: number of alleles per locus (range: 8-18)
>>    @loc.fac: locus factor for the 76 columns of @tab
>>    @all.names: list of allele names for each locus
>>    @ploidy: ploidy of each individual  (range: 2-2)
>>    @type:  codom
>>    @call: .local(x = x, i = i, j = j, loc = ..1, drop = drop)
>>
>>  // Optional content
>>    @pop: population of each individual (group size range: 9-23)
>>    @other: a list containing: xy
>>
>> *## note the difference from locNames(nancycats):*
>> *> locNames(x)*
>> *[1] "fca8"  "fca43" "fca78" "fca90" "fca96" "fca37"*
>>
>>
>> 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 Ana
>> Verissimo [verissimoac at gmail.com]
>> *Sent:* 20 July 2015 15:58
>> *To:* adegenet-forum at lists.r-forge.r-project.org
>> *Subject:* [adegenet-forum] How can I filter out loci out of HWE from a
>> genind object?
>>
>>    Hi all,
>>
>>  I have a data set comprised on 1000s of SNP loci genotyped for 10s of
>> individuals. I have tested loci for conformance to HWE and want to filter
>> out those loci out of HWE.
>>
>>  Is there a function already available to perform this filtering in
>> genind objects?
>> If not, I am guessing I may need to figure out a way to subset my data
>> using a list of loci that I want to keep?
>>
>>  Any tips or suggestions are welcome!
>> Ana
>>
>>
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>
>
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