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BioSeqClass (version 1.30.0)

featureGapPairComposition: Feature Coding by g-spaced aminoacids/bases pairs

Description

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

Usage

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

Arguments

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.

Details

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).

Examples

Run this code
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"))
}

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