polysat (version 1.7-7)

genambig.to.genbinary: Convert Between Genotype Object Classes

Description

These functions convert back and forth between the genambig and genbinary classes.

Usage

genambig.to.genbinary(object, samples = Samples(object),
                      loci = Loci(object))
genbinary.to.genambig(object, samples = Samples(object),
                      loci = Loci(object))

Value

For genambig.to.genbinary: a genbinary object containing all of the data from object. Missing, Present, and Absent are set at their default values.

For genbinary.to.genambig: a genambig object containing all of the data from object. Missing is at the default value.

Arguments

object

The object containing the genetic dataset. A genambig object for genambig.to.genbinary, or a genbinary object for genbinary.to.genambig.

samples

An optional character vector indicating samples to include in the new object.

loci

An optional character vector indicating loci to include in the new object.

Author

Lindsay V. Clark

Details

The slots Description, Ploidies, Usatnts, PopNames, and PopInfo are transferred as-is from the old object to the new. The value in the Genotypes slot is converted from one format to the other, with preservation of allele names.

See Also

genambig, genbinary

Examples

# set up a genambig object for this example
mygen <- new("genambig", samples = c("A", "B", "C", "D"),
             loci = c("locJ", "locK"))
PopNames(mygen) <- c("PopQ", "PopR")
PopInfo(mygen) <- c(1,1,2,2)
Usatnts(mygen) <- c(2,2)
Genotypes(mygen, loci="locJ") <- list(c(178, 184, 186), c(174,186),
                                      c(182, 188, 190),
                                      c(182, 184, 188))
Genotypes(mygen, loci="locK") <- list(c(133, 135, 141),
                                      c(131, 135, 137, 143),
                                      Missing(mygen), c(133, 137))

# convert it to a genbinary object
mygenB <- genambig.to.genbinary(mygen)

# check the results
viewGenotypes(mygenB)
viewGenotypes(mygen)
PopInfo(mygenB)

# convert back to a genambig object
mygenA <- genbinary.to.genambig(mygenB)
viewGenotypes(mygenA)

# note: identical(mygen, mygenA) returns FALSE, because the alleles
# origninally input are not stored as integers, while the alleles
# produced by genbinary.to.genambig are integers.