checkDNAbcd: Evaluation of a reference library of aligned DNA barcodes

Description

This function provides an overview of the content of a reference library of aligned DNA barcodes (Sonet et al. 2013). It calculates all pairwise distances and delivers an output that can be used by the function adhocTHR.

Usage

checkDNAbcd(seq, DistModel = "K80")

Arguments

seq

an object of class "DNAbin".

DistModel

"K80" (for Kimura two-parameter) or "raw" (for p-distances) or any other nucleotide substitution model available in the function "dist.dna" (Paradis et al. 2004).

Value

mylabels: a data.frame providing both parts of the species names and the complete label of each sequence (as extracted from the first argument).
listsp: a data.frame listing the number of sequences (Nseq) and haplotypes (Nhap) for each species of the reference library.
DNAlength: a numeric vector of the sequence lengths of each DNA sequence.
dist: a matrix of all distances obtained by pairwise comparison.
spdist: a list of all pairwise interspecific distances (inter) and all pairwise intraspecific distances (intra).
seq: an object of class "DNAbin" with all sequences in the reference library (= first argument).

References

Paradis E, Claude J, Strimmer K (2004) APE: analyses of phylogenetics and evolution in R language. Bioinformatics 20: 289-290.

Sonet G, Jordaens K, Nagy ZT, Breman FC, De Meyer M, Backeljau T, Virgilio M (2013) Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification. Zookeys.

Examples

Run this code

data(tephdata);
out1<-checkDNAbcd(tephdata);
layout(matrix(c(1:4),1,4));
hist(out1$DNAlength,main="Seq. lengths",xlab="Seq. length (bp)");
hist(out1$spdist$inter,main="Intersp. dist",xlab="Distance",col="#0000ff99");
hist(out1$spdist$intra, main="Intrasp. dist.",xlab="Distance",col="#0000ff22");
hist(out1$spdist$inter,main="Intra- & intersp. dist",xlab="Distance",col="#0000ff99");
hist(out1$spdist$intra, add=TRUE,col="#0000ff22");