featurePseudoAAComp: Feature Coding by Pseudo Amino Acid Composiion
In BioSeqClass: Classification for Biological Sequences

Description Usage Arguments Details Author(s) Examples

Protein sequences are coded by pseudo amino acid composiion.

1	featurePseudoAAComp(seq,d,w=0.05)

`seq`	a string vector for the protein, DNA, or RNA sequences.
`d`	an integer used as paramter of `featurePseudoAAComp` (d>=1). Coupling between amino acids X(i) and X(i+d) are considered as features.
`w`	a numeric value for the weight factor of sequence order effect in `featurePseudoAAComp`.

featurePseudoAAComp returns a matrix representing the pseudo amino acid composiion. Each row represented features of one sequence coding by a 20+d dimension numeric vector. The first 20 features indicates the composition of 20 amino acids. The last d features indicates the coupling between amino acids X(i) and X(i+d). Coupling value is cacluated by hydrophobicity, hydrophilicity and mass of amino acids.

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]
    
  PAC4 = featurePseudoAAComp(seq,4)    
}