BioSeqClass (version 1.30.0)

featureFragmentComposition: Feature Coding by the composition of k-mer fragments

Description

Sequences are coded based on the frequency of k-mer sequence fragments.

Usage

featureFragmentComposition(seq,k,class=elements("aminoacid"))

Arguments

seq

a string vector for the protein, DNA, or RNA sequences.

k

an integer indicating the length of sequence fragment (k>=1).

class

a list for the class of biological properties. It can be produced by elements and aaClass.

Details

featureFragmentComposition returns a matrix with M\^k columns. Each row represented features of one sequence coding by a M\^k dimension numeric vector. Each column is the frequency of k-mer sequence fragment.

Examples

if(interactive()){
  file = file.path(path.package("BioSeqClass"), "example", "acetylation_K.pos40.pep")
  seq = as.matrix(read.csv(file,header=F,sep="\t",row.names=1))[,1]
  
  FC2 = featureFragmentComposition(seq,2,aaClass("aaS"))
  FC3 = featureFragmentComposition(seq,3,aaClass("aaS"))
}