polysat (version 1.7-7)

editGenotypes: Edit Genotypes Using the Data Editor

Description

The genotypes from an object of one of the subclasses of gendata are converted to a data frame (if necessary), then displayed in the data editor. After the user makes the desired edits and closes the data editor window, the new genotypes are written to the gendata object and the object is returned.

Usage

editGenotypes(object, maxalleles = max(Ploidies(object)),
              samples = Samples(object), loci = Loci(object))

Value

An object identical to object but with edited genotypes.

Arguments

object

An object of the class genambig or genbinary. Contains the genotypes to be edited.

maxalleles

Numeric. The maximum number of alleles found in any given genotype. The method for genambig requires this information in order to determine how many columns to put in the data frame.

samples

Character or numeric vector indicating which samples to edit.

loci

Character or numeric vector indicating which loci to edit.

Author

Lindsay V. Clark

Details

The method for genambig lists sample and locus names in each row in order to identify the genotypes. However, only the alleles themselves should be edited. NA values and duplicate alleles in the data editor will be omitted from the genotype vectors that are written back to the genambig object.

See Also

viewGenotypes, Genotype<-, Genotypes<-

Examples

if(interactive()){  #this line included for automated checking on CRAN

# set up "genambig" object to edit
mygen <- new("genambig", samples = c("a", "b", "c"),
             loci = c("loc1", "loc2"))
Genotypes(mygen, loci="loc1") <- list(c(133, 139, 142),
                                      c(130, 136, 139, 145),
                                      c(136, 142))
Genotypes(mygen, loci="loc2") <- list(c(202, 204), Missing(mygen),
                                      c(200, 206, 208))
mygen <- reformatPloidies(mygen, output="one")
Ploidies(mygen) <- 4

# open up the data editor
mygen <- editGenotypes(mygen)

# view the results of your edits
viewGenotypes(mygen)

}