mll-method: Access and manipulate multilocus lineages.

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

Access and manipulate multilocus lineages.

Description

The following methods allow the user to access and manipulate multilocus lineages in genclone or snpclone objects.

Usage

mll(x, type = NULL)

nmll(x, type = NULL)

mll(x) <- value

Arguments

x	a genclone or snpclone object.
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.

Details

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

Value

an object of the same type as x.

Author(s)

Zhian N. Kamvar

See Also

mll.custom mlg.table

Examples

data(partial_clone)
pc <- as.genclone(partial_clone)
mll(pc)
mll(pc) <- "custom"
mll(pc)
mll.levels(pc) <- LETTERS
mll(pc)

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