The following methods allow the user to access and manipulate multilocus lineages in genclone or snpclone objects.
mll(x, type = NULL) nmll(x, type = NULL) mll(x) <- value
x | |
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type | a character specifying "original", "contracted", or "custom" defining they type of mlgs to return. Defaults to what is set in the object. |
value | a character specifying which mlg type is visible in the object. See details. |
an object of the same type as x.
genclone and snpclone objects have a slot for an internal class of object called MLG. This class allows the storage of flexible mll definitions:
"original" - naive mlgs defined by string comparison. This is default.
"contracted" - mlgs defined by a genetic distance threshold.
"custom" - user-defined MLGs
#> [1] 8 9 23 24 22 21 10 3 22 11 24 9 25 4 12 2 14 1 9 9 9 26 7 13 23 #> [26] 3 17 22 6 20 22 12 5 25 13 21 15 13 13 13 2 19 18 13 23 16 1 11 25 4mll(pc) <- "custom" mll(pc)#> [1] 8 9 23 24 22 21 10 3 22 11 24 9 25 4 12 2 14 1 9 9 9 26 7 13 23 #> [26] 3 17 22 6 20 22 12 5 25 13 21 15 13 13 13 2 19 18 13 23 16 1 11 25 4 #> 26 Levels: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 ... 26#> [1] H I W X V U J C V K X I Y D L B N A I I I Z G M W C Q V F T V L E Y M U O M #> [39] M M B S R M W P A K Y D #> Levels: A B C D E F G H I J K L M N O P Q R S T U V W X Y Z