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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
nmll(x, type = NULL)
mll(x) <- value
a '>genclone or '>snpclone object.
a character specifying "original", "contracted", or "custom" defining they type of mlgs to return. Defaults to what is set in the object.
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
mll.custom mlg.table
mll.custom
mlg.table
# NOT RUN { data(partial_clone) pc <- as.genclone(partial_clone) mll(pc) mll(pc) <- "custom" mll(pc) mll.levels(pc) <- LETTERS mll(pc) # }
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