R: Evaluation of a reference library of aligned DNA barcodes
checkDNAbcd
R Documentation
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
checkDNAbcd returns a list of 6 components:
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).
Author(s)
Gontran Sonet
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.