featurePseudoAAComp {BioSeqClass} | R Documentation

## Feature Coding by Pseudo Amino Acid Composiion

### Description

Protein sequences are coded by pseudo amino acid composiion.

### Usage

      featurePseudoAAComp(seq,d,w=0.05)

### Arguments

`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`.

### Details

`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.

### Author(s)

Hong Li

### 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]

      PAC4 = featurePseudoAAComp(seq,4)
    }

[Package BioSeqClass version 1.40.0 Index]