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

[Vikram Chhatre]

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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