bbsik {BarcodingR}

Bp Barcoding Species Identify using Kmer

Description

Species identification using BP-based method for both protein-coding barcodes, for instance, COI, and non-coding barcodes, such as, ITS, using kmer statistics.

Usage

bbsik(ref, que, kmer = kmer, UseBuiltModel = FALSE, lr = 5e-05, maxit = 1e+06)

Arguments

ref

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

que

object of class "DNAbin", which needs to be inferred.

kmer

a numeric indicating the length of kmer used.

UseBuiltModel

logic value to indicate whether a built model is used or not.

lr

parameter for weight decay. Default 5e-5.

maxit

maximum number of iterations. Default 1e+6.

Value

a list containing model parameters used, species identification success rates using references, query sequences, species inferred, and corresponding confidence levels (bp probability for BP-based method).

Author(s)

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

References

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://academic.oup.com/sysbio/article/57/2/202/1622290

Examples

data(TibetanMoth) 
ref<-as.DNAbin(as.character(TibetanMoth[1:50,]))
que<-as.DNAbin(as.character(TibetanMoth[51:60,]))
out<-bbsik(ref, que, kmer = 1, UseBuiltModel = FALSE)
out
out$convergence
out$success.rates.ref

data(pineMothITS2) 
ref<-pineMothITS2
que<-pineMothITS2
out<-bbsik(ref, que, kmer = 1, UseBuiltModel = FALSE)
out
out$convergence
out$success.rates.ref