featureFragmentComposition: Feature Coding by the composition of k-mer fragments
In BioSeqClass: Classification for Biological Sequences

Description Usage Arguments Details Author(s) Examples

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

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

`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`.

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.

Hong Li

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"))
}