BioSeqClass (version 1.30.0)

featureCKSAAP: Feature Coding by k-spaced Aminoacids/Base Pairs

Description

Protein sequences are coded based on the frequency of k-spaced aminoacids/base pairs.

Usage

featureCKSAAP(seq,g,class=elements("aminoacid"))

Arguments

seq

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

g

an integer indicating the distance between two aminoacids/bases (g>=0).

class

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

Details

featureCKSAAP returns a matrix with (g+1)*M\^2 columns. Each row represented features of one sequence coding by a (g+1)*M\^2 dimension numeric vector. Each column is the number of k-spaced aminoacids/base pair (0

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]
    
  CKSAAP0 = featureCKSAAP(seq,0,elements("aminoacid"))
  CKSAAP2 = featureCKSAAP(seq,2,elements("aminoacid"))  
}