[adegenet-forum] Removing individuals from genind obj

Caitlin Collins caitiecollins at gmail.com
Thu Oct 29 10:09:57 CET 2015

Hi again,

You might also find it useful to take a look through the tutorials posted
on the adegenet github page
<https://github.com/thibautjombart/adegenet/wiki/Tutorials>. The "basics"
tutorial contains the answer to your question (and many more like it!).


On Thu, Oct 29, 2015 at 8:33 AM, Caitlin Collins <caitiecollins at gmail.com>

> Hi Shannon,
> When you attempted to remove individuals from the genind object by working
> on the @tab slot (the second step you showed above), what you are really
> doing is asking to only remove them from the data matrix stored in the @tab
> slot, and not from all of the meta-information so lovingly stored in other
> slots of the object.
> The solution is to work with the genind object in its entirety, not just
> the @tab slot. With the object names you are using, I think this should
> work:
>      # create list of individuals (rows) to remove from @tab slot (and
> all of the other slots!!)
>      removeInd <- c("Ind5", "Ind10", "Ind60")
>      # remove individuals from *genind object*
>      # note that in this step there's no longer a comma needed before the
> closing square bracket
>      data <- data[!row.names(data at tab) %in% removeInd]
> Hope that does the trick!
> All the best,
> Caitlin.
> On Thu, Oct 29, 2015 at 4:40 AM, Shannon O'Leary <
> shannon.j.oleary at gmail.com> wrote:
>> Hi,
>> During my data analysis I have identified individuals that I want to
>> remove from the genind object - as opposed to removing those individuals
>> from my genepop file and re-reading it back into R as a genind object.
>> I created a list of individual names (I formatted the genind object so
>> that the individuals are named according to my sample names) and used it to
>> subset the matrix stored in the @tab slot.
>>      # create list of individuals (rows) to remove from @tab slot
>>      removeInd <- c("Ind5", "Ind10", "Ind60")
>>      # remove individuals from @tab slot
>>      data at tab <- data at tab[!row.names(data at tab) %in% removeInd,]
>> When I check the dimensions of the @tab slot and the number of
>> individuals in the genind object, the returned number indicate that the
>> individuals in the list have been removed from the genind object.
>>      # number of rows and columns in @tab slot
>>      dim(GTF_genotypes at tab)
>>      # number of Individuals in genind object
>>      nInd(GTF_genotypes)
>> But when I check the length of the vector stored in the @pop slot it
>> hasn't changed, same for the information @strata slot.
>>      # number of individuals in @pop slot
>>      length(GTF_genotypes at pop)
>> Is there a way to remove individuals from the genind object so that that
>> change is then reflected in all the slots of the genind object?
>> Thanks,
>> Shannon
>> ------------------------------------------------------------------------
>> Shannon J. O'Leary
>> Postdoctoral Research Associate
>> Marine Genomics Lab
>> Harte Research Institute for Gulf of Mexico Studies
>> Texas A&M Corpus Christi
>> _______________________________________________
>> adegenet-forum mailing list
>> adegenet-forum at lists.r-forge.r-project.org
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