featureAAindex {BioSeqClass} | R Documentation

## Feature Coding by physicochemical/biochemical properties in AAindex

### Description

Protein sequences are coded based on the physicochemical/biochemical properties of amino acids in AAindex database.

### Usage

      featureAAindex(seq,aaindex.name="all")
      featureACI(seq,aaindex.name="all")
      featureACF(seq,n,aaindex.name="all")

### Arguments

`seq` | a string vector for the protein, DNA, or RNA sequences.
`aaindex.name` | a string for the name of physicochemical and biochemical properties in AAindx.
`n` | an integer used as paramter of `featureACF` (1<=n<=L-2, L is the the length of sequence). featureACF takes the auto-correlation between fragment X(1)...X(L-m) and X(m+1)...X(L) (1<=m<=n) as features.

### Details

`featureAAindex` returns a matrix measuring the physicochemical and biochemical properties of amino acids by AAindex (http://www.genome.jp/aaindex). If parameter aaindex.name="all", all properties in AAindex will be considered, and each row represented the features of one sequence coding by a 531*N dimension numeric vector. If parameter aaindex.name is a name of property in AAindex, each row represented the features of one sequence coding by a N dimension numeric vector.

`featureACI` returns a matrix with 531 columns, measuring the average cumulative value of AAindex. N is the length of input sequence, and N must be odd. Central residue of all windows are the central residue of input sequence. Each column is the average cumulative AAindex over a sliding window.

`featureACF` returns a matrix with 531*n columns, measuring the Auto-Correlation Function (ACF) of AAindex. If parameter aaindex.name is a name of property in AAindex, each row represented the features of one sequence coding by a n dimension numeric vector.

### 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]

      AI_all = featureAAindex(seq)
      AI_ANDN920101 = featureAAindex(seq,"ANDN920101")

      ACI_all = featureACI(seq)
      ACI_ANDN920101 = featureACI(seq,"ANDN920101")

      ACF_all_1 = featureACF(seq,1)
      ACF_ANDN920101_3 = featureACF(seq,3,"ANDN920101")
    }

[Package BioSeqClass version 1.40.0 Index]