R: Edit Genotypes Using the Data Editor

editGenotypes {polysat} | R Documentation

## 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))

### 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.

### 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.

### Value

An object identical to `object` but with edited genotypes.

### Author(s)

Lindsay V. Clark

### 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)

    }

[Package polysat version 1.7-6 Index]