featureGapPairComposition: Feature Coding by g-spaced aminoacids/bases pairs
In BioSeqClass: Classification for Biological Sequences

Description Usage Arguments Details Author(s) Examples

Sequences are coded based on the frequency of g-spaced aminoacids/bases pairs.

1	featureGapPairComposition(seq,g,class=elements("aminoacid"))

`seq`	a string vector for the protein, DNA, or RNA sequences.
`g`	an integer indicating the distance between two aminoacids/bases (g>=0).
`class`	a list for the class of biological properties. It can be produced by `elements` and `aaClass`.

featureGapPairComposition returns a matrix with M\^2 columns. Each row represented features of one sequence coding by a M\^2 dimension numeric vector. Each column is the frequency of g-spaced aminoacids/bases pair. featureFragmentComposition(seq,2) is same with featureGapPairComposition(seq,0).

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]
  
  GPC0 = featureGapPairComposition(seq,0,elements("aminoacid"))
  GPC2 = featureGapPairComposition(seq,2,elements("aminoacid"))
}