[adegenet-forum] Removing individuals from genind obj

Shannon O'Leary shannon.j.oleary at gmail.com
Thu Oct 29 05:40:02 CET 2015


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
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