Answer to: Counting instances of genotype strings where order is irrelevant within locus

A quick one-liner using Tmisc::strSort (same basic approach of sorting the strings before using table): library(Tmisc) table(strSort(unlist(offspring, 0, 0))) #> #> aabb aabB aaBB aAbb aAbB aABB AAbb AAbB AABB #> 1 2 1 2 4 2 1 2 1 A faster option if performance is a concern. This uses the non-sorting unordered match approach found in this answer. strtable <- function(x) { x <- unlist(x, 0, 0) y <- mapply(utf8ToInt, x, USE.NAMES = FALSE) u <- unique(`dim<-`(y, NULL)) y[] <- match(y, u) y <- colSums(y*sin(y*pi/(length(u) + 1))) i <- which(!duplicated(y)) `names<-`(tabulate(match(y, y[i])), x[i]) } strtable(offspring) #> AABB AAbB aABB aAbB AAbb aAbb aaBB aabB aabb #> 1 2 2 4 1 2 1 2 1 Benchmarking against the functions from @RuiBarradas and @ThomasIsCoding (the function provided by @jay.sf does not return the correct counts for the general problem of counting occurrences of unordered strings--it assumes the OP's specific problem of "diploid, biallelic loci" as noted in jay.sf's answer). microbenchmark::microbenchmark( strtable(str), table(strSort(unlist(str, 0, 0))), Rui_Barradas(str), tic(str) ) #> Unit: milliseconds #> expr min lq mean median uq max neval #> strtable(str) 8.3294 10.06245 12.71034 12.6583 14.5268 22.7197 100 #> table(strSort(unlist(str, 0, 0))) 169.1872 215.74645 236.81358 242.0942 260.7001 325.7841 100 #> Rui_Barradas(str) 172.1685 215.09295 252.07995 252.9611 283.8306 333.5353 100 #> tic(str) 149.1786 189.83450 210.64926 213.6807 228.9248 318.0333 100 Benchmark data: str <- stringi::stri_rand_strings(1e4, 4, "[A-Ea-e]") # partial check for correctness res <- vector("list", 4) res[[1]] <- sort(as.integer(table(strSort(unlist(str, 0, 0))))) res[[2]] <- sort(as.integer(strtable(str))) res[[3]] <- sort(as.integer(Rui_Barradas(str))) res[[4]] <- sort(as.integer(tic(str))) identical(res[-1], res[-4]) #> [1] TRUE Functions: Rui_Barradas <- function(x) { lapply(x, strsplit, "") |> unlist(recursive = FALSE) |> lapply(sort) |> sapply(paste, collapse = "") |> table(useNA = "ifany") } tic <- function(x) { # ThomisIsCoding table(sapply(unlist(x), \(x) intToUtf8(utf8ToInt(x)[order(utf8ToInt(x))]))) }