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bodkan / admixr

An R package for reproducible and automated ADMIXTOOLS analyses
https://bodkan.net/admixr
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Error in F3: Following samples are not present #90

Closed ans6160 closed 1 year ago

ans6160 commented 1 year ago

Hi,

I am trying to run the f3 command over a large data set and I keep getting this error that says the following populations are not present in the data. The .snp/.ind/.geno files are all in eigenstrat format and if I were to open the files in the terminal, I see exactly what you expect to see. I was following the tutorial, but I am not sure what I am doing wrong.

Here is the code that produces the error: prefix<- "~/Downloads/AADR_datasets/F3_stats_group/f3_aDNA_subset" pre<- eigenstrat(prefix) pre #gives me the eigenstrat object

pops

pops<-setDT(list(final_ind$V3)) testRes<- f3(A=pops, B=pops, C = "Ignore_Mbuti(discovery).DG", data = pre)

Hopefully this description makes sense.

ans6160 commented 1 year ago

I figured out what was wrong. I was not specifying the column in pops.

bodkan commented 1 year ago

Great! :) Thanks for reporting back and thanks for using admixr!