featureHydro: Feature Coding by hydrophobicity

In BioSeqClass: Classification for Biological Sequences

Description

Protein sequences are coded based on their hydrophobicity.

Usage

  featureHydro(seq,hydro.method="SARAH1")
  featureACH(seq,hydro.index="hydroE")

Arguments

seq	a string vector for the protein, DNA, or RNA sequences.
hydro.method	a string for the method of coding protein hydrophobic effect. This must be one of the strings "kpm" or "SARAH1".
hydro.index	a string for the method of coding protein hydrophobic effect. This must be one of the strings "hydroE", "hydroF" or "hydroC".

Details

featureHydro returns a matrix measuring the hydrophobic effect. Parameter "hydro.method" supported following coding methods: "kpm": use a numeral to indicating the hydrophobic effect of amino acid. Each sequence is coded by a N dimension numeric vector. "SARAH1": use a 5 dimension 0-1 vector to indicating the hydrophobic effect of amino acid. Each sequence is coded by a 5*N dimension 0-1 vector.

featureACH returns a matrix with (N-1)/2 columns. N is the length of input sequence, andis N must be odd. Central residue of all windows are the central residue of input sequence. Each column is the average cumulative hydrophobicity over a sliding window.

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]
   
  H1 = featureHydro(seq,"kpm")
  H2 = featureHydro(seq,"SARAH1")

  H3 = featureACH(seq,hydro.index="hydroE")
  H3 = featureACH(seq,hydro.index="hydroF")
  H3 = featureACH(seq,hydro.index="hydroC")
}

Example output

Loading required package: scatterplot3d

BioSeqClass documentation built on April 28, 2020, 9:19 p.m.