featureHydro {BioSeqClass} | R Documentation

## Feature Coding by hydrophobicity

### 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")
    }

[Package BioSeqClass version 1.45.0 Index]