MergeIdenticalHaplotypes: Merge Alleles with Identical DNA Sequences

In polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

Merge Alleles with Identical DNA Sequences

Description

If any alleles within a locus have identical alleleNucleotides values (including those identical based on IUPAC ambiguity codes), this function merges those alleles, summing their read depths. This function is primarily intended to be used internally in cases where tags vary in length within a locus, resulting in truncated alleleNucleotides.

Usage

MergeIdenticalHaplotypes(object, ...)

Arguments

object	A RADdata object.
...	Additional arguments (none implemented).

Value

A RADdata object identical to object, but with alleles merged.

Author(s)

Lindsay V. Clark

See Also

MergeRareHaplotypes, readProcessIsoloci

Examples

data(exampleRAD)
# change a haplotype for this example
exampleRAD$alleleNucleotides[5] <- "GY"

nAlleles(exampleRAD)
exampleRAD <- MergeIdenticalHaplotypes(exampleRAD)
nAlleles(exampleRAD)

polyRAD documentation built on Nov. 10, 2022, 5:14 p.m.