[adegenet-forum] Removing individuals from genind obj
caitiecollins at gmail.com
Thu Oct 29 09:33:44 CET 2015
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
# 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,
On Thu, Oct 29, 2015 at 4:40 AM, Shannon O'Leary <shannon.j.oleary at gmail.com
> 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
> 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?
> 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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