hap_collapse: Removes Duplicated Sequences from Alignment

In delimtools: Helper Functions for Species Delimitation Analysis

Removes Duplicated Sequences from Alignment

Description

hap_collapse() collapses haplotypes from a DNAbin object, keeping unique haplotypes only.

Usage

hap_collapse(dna, clean = TRUE, collapseSubstrings = TRUE, verbose = TRUE)

Arguments

dna	A DNAbin object.
clean	logical. Whether to remove or not remove non ACTG bases from alignment.
collapseSubstrings	logical. Whether to collapse or not collapse shorter but identical sequences.
verbose	logical. Returns a warning if any sequence contains non ACTG bases. See clean_dna for details.

Details

hap_collapse() collapses a DNAbin object, keeping unique haplotypes only. If clean = TRUE, the function will call clean_dna to remove any non ACTG bases from alignment prior to collapsing haplotypes. If clean = FALSE, the function will treat data as it is, and will not remove any bases. If collapseSubstrings = TRUE, the function will consider shorter but identical sequences as the same haplotype and collapse them, returning the longest sequence. If collapseSubstrings = FALSE, the function will consider shorter but identical sequences as different haplotypes and will keep them.

Value

A DNAbin object.

Author(s)

Rupert A. Collins

Examples

# collapse into unique haplotypes, including shorter sequences
hap_collapse(geophagus, clean = TRUE, collapseSubstrings = TRUE)

# collapse into unique haplotypes keeping shorter sequences
hap_collapse(geophagus, clean = TRUE, collapseSubstrings = FALSE)

delimtools documentation built on April 3, 2025, 9:28 p.m.