a matrix of alleles as genotypes (e.g., A/A, C/G, etc.)
sep
a character which delimits the alleles in a genotype (/ or |)
NA_to_n
logical indicating whether NAs should be scores as n
x2
a vector of genotypes
split
character passed to strsplit to split the genotype into alleles
na.rm
logical indicating whether to remove NAs
as.numeric
logical specifying whether to convert to a numeric
Details
The function alleles2consensus converts genotypes to a single consensus allele using IUPAC ambiguity codes for heterozygotes.
Note that some functions, such as ape::seg.sites do not recognize ambiguity characters (other than 'n').
This means that these functions, as well as functions that depend on them (e.g., pegas::tajima.test), will produce unexpected results.
The function get.alleles takes a vector of genotypes and returns the unique alleles.