polyRAD (version 1.3)

MergeIdenticalHaplotypes: Merge Alleles with Identical DNA Sequences

Description

If any alleles within a locus have identical alleleNucleotides values, 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.

See Also

MergeRareHaplotypes, readProcessIsoloci

Examples

# NOT RUN {
data(exampleRAD)
# change a haplotype for this example
exampleRAD$alleleNucleotides[5] <- "GC"

nAlleles(exampleRAD)
exampleRAD <- MergeIdenticalHaplotypes(exampleRAD)
nAlleles(exampleRAD)
# }