optimize.kmer {BarcodingR}

Optimize kmer Length

Description

Optimize kmer length by trying kmers which length is in the range from 1 to max.kmer. The optimal kmer will have maximal species identification success rate.

Usage

optimize.kmer(ref, max.kmer = max.kmer)

Arguments

ref

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

max.kmer

a numeric to indicate the length of maximal kmer.

Value

a numeric indicating the optimal kmer in the range examined.

Author(s)

Ai-bing ZHANG, Cai-qing YANG, Meng-di HAO, CNU, Beijing, CHINA.

References

zhangab2008 (at) mail. cnu. edu. cn/zhangab2008 (at) gmail.com.

Examples

data(TibetanMoth) 
ref<-TibetanMoth[1:10,]
optimial.kmer<-optimize.kmer(ref,max.kmer=5)