extractProtMoran {Rcpi} | R Documentation

## Moran Autocorrelation Descriptor

### Description

Moran Autocorrelation Descriptor

### Usage

    extractProtMoran(x, props = c("CIDH920105", "BHAR880101", "CHAM820101",
      "CHAM820102", "CHOC760101", "BIGC670101", "CHAM810101", "DAYM780201"),
      nlag = 30L, customprops = NULL)

### Arguments

`x` | A character vector, as the input protein sequence.
`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`.
`customprops` | A `n x 21` named data frame contains `n` customize property. Each row contains one property. The column order for different amino acid types is `'AccNo'`, `'A'`, `'R'`, `'N'`, `'D'`, `'C'`, `'E'`, `'Q'`, `'G'`, `'H'`, `'I'`, `'L'`, `'K'`, `'M'`, `'F'`, `'P'`, `'S'`, `'T'`, `'W'`, `'Y'`, `'V'`, and the columns should also be exactly named like this. The `AccNo` column contains the properties' names. Then users should explicitly specify these properties with these names in the argument `props`. See the examples below for a demonstration. The default value for `customprops` is `NULL`.

### Details

This function calculates the Moran autocorrelation descriptor (Dim: `length(props) * nlag`).

### Value

A length `nlag` named vector

### Author(s)

Nan Xiao <https://nanx.me>

### 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.

### See Also

See `extractProtMoreauBroto` and `extractProtGeary` for Moreau-Broto autocorrelation descriptors and Geary autocorrelation descriptors.

### Examples

    x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]
    extractProtMoran(x)

    myprops = data.frame(AccNo = c("MyProp1", "MyProp2", "MyProp3"),
                         A = c(0.62,  -0.5, 15),  R = c(-2.53,   3, 101),
                         N = c(-0.78,  0.2, 58),  D = c(-0.9,    3, 59),
                         C = c(0.29,    -1, 47),  E = c(-0.74,   3, 73),
                         Q = c(-0.85,  0.2, 72),  G = c(0.48,    0, 1),
                         H = c(-0.4,  -0.5, 82),  I = c(1.38, -1.8, 57),
                         L = c(1.06,  -1.8, 57),  K = c(-1.5,    3, 73),
                         M = c(0.64,  -1.3, 75),  F = c(1.19, -2.5, 91),
                         P = c(0.12,     0, 42),  S = c(-0.18, 0.3, 31),
                         T = c(-0.05, -0.4, 45),  W = c(0.81, -3.4, 130),
                         Y = c(0.26,  -2.3, 107), V = c(1.08, -1.5, 43))

    # Use 4 properties in the AAindex database, and 3 cutomized properties
    extractProtMoran(x, customprops = myprops,
                     props = c('CIDH920105', 'BHAR880101',
                               'CHAM820101', 'CHAM820102',
                               'MyProp1', 'MyProp2', 'MyProp3'))

[Package Rcpi version 1.24.0 Index]