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I want to convert a genetic matrix (rows are samples, columns are alleles) into a STRUCTURE file (output .str) within R. Is there a preferred way to achieve this? I've found genind_to_structure in the graph4lg R package, but I wanted to see if there are other approaches.

An example of what I mean by a "genetic matrix":

# Build a matrix of alleles
temp <- lapply(1:30, function(i) sample(1:9, 4, replace = TRUE))
temp <- sapply(temp, paste, collapse="")
temp <- matrix(temp, nrow = 10, dimnames = list(paste("ind",1:10), paste("loc",1:3)))
temp

# Convert matrix to genind format (for adegenet package)
test <- df2genind(temp, ploidy = 4, sep = "")
test

# How to convert to STRUCTURE?

If anyone has input, please chime in! Thanks

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    $\begingroup$ Structure is a bit old now. There is fastStructure (2014) rajanil.github.io/fastStructure which is Python. Happy to do this if there's a Pythonic Bio.popgen equivalent geared for fastStructure $\endgroup$
    – M__ ♦
    Commented Jun 15, 2022 at 16:35
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    $\begingroup$ I’m not totally sure what you’re asking, since the current method seems to be working? Is there a reason why you need another approach? $\endgroup$
    – user438383
    Commented Jun 17, 2022 at 7:25

1 Answer 1

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I ultimately found this function, which I used for the purpose of converting a genind to a STRUCTURE file. The graph4lg genind_2_structure command would regularly error on me (present working directory couldn't be passed as the output argument).

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