Description Usage Arguments Value Author(s) See Also Examples
This function will allow you to define custom multilocus lineages for your data set.
1 2 3 4 5 6 7 | mll.custom(x, set = TRUE, value)
mll.custom(x, set = TRUE) <- value
mll.levels(x, set = TRUE, value)
mll.levels(x, set = TRUE) <- value
|
x |
a genclone or snpclone object. |
set |
logical. If |
value |
a vector that defines the multilocus lineages for your data. This can be a vector of ANYTHING that can be turned into a factor. |
an object of the same type as x
Zhian N. Kamvar
1 2 3 4 5 6 7 8 9 10 11 12 | data(partial_clone)
pc <- as.genclone(partial_clone)
mll.custom(pc) <- LETTERS[mll(pc)]
mll(pc)
# Let's say we had a mistake and the A mlg was actually B.
mll.levels(pc)[mll.levels(pc) == "A"] <- "B"
mll(pc)
# Set the MLL back to the original definition.
mll(pc) <- "original"
mll(pc)
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