featureCTD {BioSeqClass} | R Documentation

## Feature Coding by composition, transition and distribution

### Description

Sequences are coded based on their composition, transition and distribution.

### Usage

      featureCTD(seq,class=elements("aminoacid"))

### Arguments

`seq` | a string vector for the protein, DNA, or RNA sequences.
`class` | a list for the class of biological properties. It can be produced by `elements` and `aaClass`.

### Details

`featureCTD` returns a matrix with M+M*(M-1)/2+M*5 columns. Each row represented features of one sequence coding by a M+M*(M-1)/2+M*5 dimension numeric vector. Three kinds of coding: composition (C), transition (T) and distribution (D) are used. C is the number of amino acids of a particular property (such as hydrophobicity) divided by the total number of amino acids. T characterizes the percent frequency with which amino acids of a particular property is followed by amino acids of a different property. D measures the chain length within which the first, 25, 50, 75 and 100 acids of a particular property is located respectively.

### Author(s)

Hong Li

### Examples

    if(interactive()){
      file = file.path(path.package("BioSeqClass"), "example", "acetylation_K.fasta")
      library(Biostrings)
      tmp = readAAStringSet(file)

      proteinSeq = as.character(tmp)

      CTD1 = featureCTD(proteinSeq, class=elements("aminoacid") )
      CTD2 = featureCTD(proteinSeq, class=aaClass("aaV") )
    }

[Package BioSeqClass version 1.38.0 Index]