zkamvar
commented
2 years ago Hello,
It depends on what you are looking for. If you want a genotype table that gives you the allele calles, you want the {adegenet} function, genind2df() if you want the ID of the assigned MLG, then you need to use the mll() (multilocus lineage) function. If, however, you want to know what isolates are associated with a single MLG, then you want mlg.id()
library(poppr)
library(tibble)
data(Aeut)
Aeut <- as.genclone(Aeut)
tibble(genind2df(Aeut)) # genotype table
#> # A tibble: 187 × 57
#> pop L01 L02 L03 L04 L05 L06 L07 L08 L09 L10 L11 L12
#> <fct> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int> <int>
#> 1 Athe… 1 0 1 0 1 0 0 1 1 0 1 1
#> 2 Athe… 1 0 1 0 0 0 0 1 1 1 1 1
#> 3 Athe… 1 0 1 0 0 0 0 0 1 0 1 1
#> 4 Athe… 1 0 1 0 0 0 0 0 1 0 1 1
#> 5 Athe… 1 0 1 0 0 0 0 0 1 0 1 1
#> 6 Athe… 1 0 1 0 0 0 0 0 1 1 1 1
#> 7 Athe… 1 0 1 0 0 0 0 0 1 0 1 1
#> 8 Athe… 1 0 1 0 0 0 0 0 1 0 1 1
#> 9 Athe… 1 0 1 0 0 0 0 0 1 0 1 1
#> 10 Athe… 1 1 0 0 0 0 0 0 1 0 1 0
#> # … with 177 more rows, and 44 more variables: L13 <int>, L14 <int>, L15 <int>,
#> # L16 <int>, L17 <int>, L18 <int>, L19 <int>, L20 <int>, L21 <int>,
#> # L22 <int>, L23 <int>, L24 <int>, L25 <int>, L26 <int>, L27 <int>,
#> # L28 <int>, L29 <int>, L30 <int>, L31 <int>, L32 <int>, L33 <int>,
#> # L34 <int>, L35 <int>, L36 <int>, L37 <int>, L38 <int>, L39 <int>,
#> # L40 <int>, L41 <int>, L42 <int>, L43 <int>, L44 <int>, L45 <int>,
#> # L46 <int>, L47 <int>, L48 <int>, L49 <int>, L50 <int>, L51 <int>, …
tibble(isolate = indNames(Aeut), MLG = mll(Aeut)) # table of MLG id for each isolate
#> # A tibble: 187 × 2
#> isolate MLG
#> <chr> <int>
#> 1 001 63
#> 2 002 53
#> 3 003 17
#> 4 004 16
#> 5 005 26
#> 6 006 42
#> 7 007 8
#> 8 008 17
#> 9 009 16
#> 10 010 93
#> # … with 177 more rows
mlg.id(Aeut)["59"] # List of isolates for each MLG
#> $`59`
#> [1] "057" "159"Created on 2022-05-23 by the reprex package (v2.0.1)
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Please include a brief description of the problem with a code example: I checked the manual and vignette for a command that would do this but I could find it. IS the multilocus info stored in the original object (data file) can it be extracted as a table?
THANK YOU very much, IN ADVANCE!