reducePloidy: Reduce the ploidy of an object of class genalex

In douglasgscofield/readGenalex: Read, Write, Manipulate and Convert GenAlEx-Format Genotype Files

Description

Reduce the ploidy of an object of class genalex. Currently restricted to reducing the ploidy of diploid data to haploid by selecting only the first allele of each locus.

Usage

## S3 method for class 'genalex'
reducePloidy(x, new.ploidy = 1, ...)

Arguments

x	An annotated data frame of class genalex
new.ploidy	The desired new ploidy. Currently, the only usefully accepted value is 1, with ploidy of x being 2; a ploidy matching the current ploidy of x silently returns x.
...	Additional arguments, currently ignored

Details

This function reduced the ploidy of a data frame of class genalex data frame by selecting the first allele of each locus. Occasionally haploid data is encoded in GenAlEx datasets by using homozygous diploid loci, and this is a useful function for making these truly haploid.

Value

A data frame of class genalex containing genotype data from x reduced to the specified new.ploidy, with attributes updated as required.

Author(s)

Douglas G. Scofield

Examples

data(Qagr_adult_genotypes)
attr(Qagr_adult_genotypes, "ploidy")
p1 <- reducePloidy(Qagr_adult_genotypes, 1)

douglasgscofield/readGenalex documentation built on May 15, 2019, 10:43 a.m.