subset_genepop
JHHartman opened this issue · comments
Hello, I am trying to use subset_genepop to subset a set of loci names using "subs" in the getTopLoc function. When I get to this part of the code: genepopedit::subset_genepop(genepop = sub_data_path, subs = FST.Filter.Vec, keep = TRUE, path = paste0(path.start, "/", "subset_for_LD.txt")) I receive the error: "Error in [.data.frame(temp2, , c(subs, "Pop")) : undefined columns selected" I tried to run this piece of code outside of the getTopLoc function and I still couldn't get it to work. Has Anyone else had this problem/know how to fix it?
Reading through the tealeaves this could be one of two things. 1) geneopedit can't discriminate the populations from within the SampleIDs. The format we had to force was a unique population name and a unique number separated by an underscore (e.g., ABC_01 will be picked up as population ABC and sample 01, but a sampleID entered as ABC01 would not work). Or it could be that the vector FST.Filter.Vec has a loci name (or names) not matching up with the genepop file in sub_data_path.
Try this:
setdiff(genepop_detective(sub_data_path,"Loci"),FST.Filter.Vec)
that should flag any loci names that don't match.
Also note that we have pushed a small update to hybriddetective, which should alleviate the indexing error that creeped up with a data.table update. If you re-install it should hopefully work better.