polyRAD (version 1.1)

MergeRareHaplotypes: Consolidate Reads from Rare Alleles

Description

MergeRareHaplotypes searches for rare alleles in a "RADdata" object, and merges them into the most similar allele at the same locus based on nucleotide sequence (or the most common allele if multiple are equally similar). Read depth is summed across merged alleles, and the alleleNucleotides slot of the "RADdata" object contains IUPAC ambiguity codes to indicate nucleotide differences across merged alleles. This function is designed to be used immediately after data import.

Usage

MergeRareHaplotypes(object, ...)
# S3 method for RADdata
MergeRareHaplotypes(object, min.ind.with.haplotype = 10, …)

Arguments

object

A "RADdata" object.

min.ind.with.haplotype

The minimum number of taxa having reads from a given allele for that allele to not be merged.

…

Additional arguments; none implemented.

Value

A "RADdata" object identical to object, but with its $alleleDepth, $antiAlleleDepth, $depthRatio, $depthSamplingPermutations, $alleleNucleotides, and $alleles2loc arguments adjusted after merging alleles.

Details

Alleles with zero reads across the entire dataset are removed by MergeRareHaplotypes without merging nucleotide sequences. After merging, at least one allele is left, even if it has fewer than min.ind.with.haplotype taxa with reads, as long as it has more than zero taxa with reads.

See Also

SubsetByLocus, VCF2RADdata, readStacks

Examples

# NOT RUN {
data(exampleRAD)
exampleRAD2 <- MergeRareHaplotypes(exampleRAD, 
                                   min.ind.with.haplotype = 12)
exampleRAD$alleleDepth[21:30,3:5]
exampleRAD2$alleleDepth[21:30,3:4]
exampleRAD$alleleNucleotides
exampleRAD2$alleleNucleotides
# }