calculateAutocor {HPiP} | R Documentation

## Calculate Autocorrelation Descriptors

### Description

This function calculates autocorrelation descriptors:

- `moran` - moran autocorrelation, (Dim: `length(target.props) * nlag`).

- `geary` - geary autocorrelation, (Dim: `length(target.props) * nlag`).

- `moreaubroto` - moreau-broto autocorrelation, (Dim: `length(target.props) * nlag`).

### Usage

    calculateAutocor(
      x,
      target.props = c("CIDH920105", "BHAR880101", "CHAM820101", "CHAM820102",
        "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"),
      nlag = 30L,
      type = c("moran", "geary", "moreaubroto")
    )

### Arguments

`x` | A data.frame containing gene/protein names and their fasta sequences.
`target.props` | A character vector, specifying the accession number of the target properties. 8 properties are used by default, as listed below: AccNo. CIDH920105 Normalized average hydrophobicity scales (Cid et al., 1992) AccNo. BHAR880101 Average flexibility indices (Bhaskaran-Ponnuswamy, 1988) AccNo. CHAM820101 Polarizability parameter (Charton-Charton, 1982) AccNo. CHAM820102 Free energy of solution in water, kcal/mole (Charton-Charton, 1982) AccNo. CHOC760101 Residue accessible surface area in tripeptide (Chothia, 1976) AccNo. BIGC670101 Residue volume (Bigelow, 1967) AccNo. CHAM810101 Steric parameter (Charton, 1981) AccNo. DAYM780201 Relative mutability (Dayhoff et al., 1978b)
`nlag` | Maximum value of the lag parameter. Default is `30`.
`type` | The autocorrelation type: `moran`, `geary`, or `moreaubroto`.

### Details

calculateAutocor

### Value

A length `nlag` named vector for data input.

### Author(s)

Matineh Rahmatbakhsh <matinerb.94@gmail.com>, Nan Xiao

### References

AAindex: Amino acid index database. http://www.genome.ad.jp/dbget/aaindex.html

Feng, Z.P. and Zhang, C.T. (2000) Prediction of membrane protein types based on the hydrophobic index of amino acids. Journal of Protein Chemistry, 19, 269-275.

Horne, D.S. (1988) Prediction of protein helix content from an autocorrelation analysis of sequence hydrophobicities. Biopolymers, 27, 451-477.

Sokal, R.R. and Thomson, B.A. (2006) Population structure inferred by local spatial autocorrelation: an Usage from an Amerindian tribal population. American Journal of Physical Anthropology, 129, 121-131.

### Examples

    data(UP000464024_df)
    x_df <- calculateAutocor(UP000464024_df,type = 'moran')
    head(x_df, n = 2L)

[Package HPiP version 1.0.0 Index]