coercion-methods: Switch between genind and genclone objects.

In poppr: Genetic Analysis of Populations with Mixed Reproduction

Switch between genind and genclone objects.

Description

as.genclone will create a genclone object from a genind object OR anything that can be passed to the genind initializer.

Usage

bootgen2genind(bg)

as.genclone(x, ..., mlg, mlgclass = TRUE)

genclone2genind(x)

as.genambig(x)

Arguments

bg	a bootgen object
x	a genind or genclone object
...	arguments passed on to the genind constructor
mlg	an optional vector of multilocus genotypes as integers
mlgclass	should the mlg slot be of class MLG?

Details

genclone2genind will remove the mlg slot from the genclone object, creating a genind object.

as.genambig will convert a genind or genclone object to a polysat genambig class.

Author(s)

Zhian N. Kamvar

See Also

splitStrata, genclone, read.genalex aboot

Examples

data(Aeut)
Aeut

# Conversion to genclone --------------------------------------------------
Aeut.gc <- as.genclone(Aeut)
Aeut.gc

# Conversion to genind ----------------------------------------------------
Aeut.gi <- genclone2genind(Aeut.gc)
Aeut.gi

# Conversion to polysat's "genambig" class --------------------------------
if (require("polysat")) {
  data(Pinf)
  Pinf.gb <- as.genambig(Pinf)
  summary(Pinf.gb)
}

data(nancycats)

# Conversion to bootgen for random sampling of loci -----------------------
nan.bg  <- new("bootgen", nancycats[pop = 9])
nan.bg

# Conversion back to genind -----------------------------------------------
nan.gid <- bootgen2genind(nan.bg)
nan.gid

poppr documentation built on March 31, 2023, 7:15 p.m.