DNAbin2kmerFreqMatrix {BarcodingR}

Calculation of Kmer Frequency Matrix from DNAbin for Both Reference and Query Sequences

Description

Calculation of kmer frequency matrices from DNAbin for both reference and query sequences.

Usage

DNAbin2kmerFreqMatrix(ref, que, kmer = kmer)

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 to indicate the length of kmer used.

Value

kmer frequency matrices for both ref and que sequences, but only based on kmers found in ref!!! new kmers in que will be ignored.

Author(s)

Ai-bing ZHANG, PhD. CNU, Beijing, CHINA. zhangab2008(at)mail.cnu.edu.cn

References

zhangab2008(at)mail.cnu.edu.cn

Examples

data(TibetanMoth) 
ref<-as.DNAbin(as.character(TibetanMoth[1:50,]))
que<-as.DNAbin(as.character(TibetanMoth[51:60,]))
out<-DNAbin2kmerFreqMatrix(ref,que,kmer=3)
out