barcoding.spe.identify2 {BarcodingR}

Species Identification Based on Fuzzy-set Method and kmer

Description

Species identification based on fuzzy-set method (Zhang et al. 2012)and kmer.

Usage

barcoding.spe.identify2(ref, que, kmer = kmer, optimization = TRUE)

Arguments

ref

object of class "DNAbin" used as a reference dataset, which contains taxon information.

que

object of class "DNAbin", whose identities (species names) need to be inferred.

kmer

a numeric to indicate the length of maximum kmer to try in the range of 1 to kmer in case of optimization = TRUE, otherwise, only a certain length of kmer is used.

optimization

a character string, indicating whether different length of kmer (up to kmer) will be used or just a specified length of kmer will be used.

Value

a list indicating the identified species.

Note

read.dna() from package ape was used to obtain DNAbin object for unaligned non-coding barcodes.

Author(s)

Ai-bing ZHANG, Cai-qing YANG, Meng-di HAO, CNU, Beijing, CHINA, contact at zhangab2008 (at) mail. cnu. edu. cn.

References

Zhang, A. B., M. D. Hao, C. Q. Yang, and Z. Y. Shi. (2017). BarcodingR: an integrated R package for species identification using DNA barcodes. Methods Ecol Evol. 8(5):627-634. https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.12682.

Jin,Q., H.L. Han, X.M. Hu, X.H. Li,C.D. Zhu,S. Y. W. Ho, R. D. Ward, A.B. Zhang . (2013). Quantifying Species Diversity with a DNA Barcoding-Based Method: Tibetan Moth Species (Noctuidae) on the Qinghai-Tibetan Plateau. PloS One 8: e644. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064428.

Zhang, A. B., C. Muster, H.B. Liang, C.D. Zhu, R. Crozier, P. Wan, J. Feng, R. D. Ward.(2012). A fuzzy-set-theory-based approach to analyse species membership in DNA barcoding. Molecular Ecology, 21(8):1848-63. https://onlinelibrary.wiley.com/doi/10.1111/j.1365-294X.2011.05235.x

Zhang, A. B., D. S. Sikes, C. Muster, S. Q. Li. (2008). Inferring Species Membership using DNA sequences with Back-propagation Neural Networks. Systematic Biology, 57(2):202-215. https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.12682

Examples

data(pineMothITS2) 
ref<-pineMothITS2
que<-ref
spe.id<-barcoding.spe.identify2(ref,que, kmer = 1, optimization = FALSE)
spe.id