mll.custom: Define custom multilocus lineages

In grunwaldlab/poppr: Genetic Analysis of Populations with Mixed Reproduction

Define custom multilocus lineages

Description

This function will allow you to define custom multilocus lineages for your data set.

Usage

mll.custom(x, set = TRUE, value)

mll.custom(x, set = TRUE) <- value

mll.levels(x, set = TRUE, value)

mll.levels(x, set = TRUE) <- value

Arguments

x	a genclone or snpclone object.
set	logical. If TRUE (default), the visible mlls will be set to 'custom'.
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.

Value

an object of the same type as x

Author(s)

Zhian N. Kamvar

See Also

mll mlg.table

Examples

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)

grunwaldlab/poppr documentation built on March 18, 2024, 11:24 p.m.