featureAAindex: Feature Coding by physicochemical/biochemical properties in...
In BioSeqClass: Classification for Biological Sequences

Description Usage Arguments Details Author(s) Examples

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

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

`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.

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.

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]
 
  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") 
}