extractProtAPAAC {Rcpi} | R Documentation

## Amphiphilic Pseudo Amino Acid Composition Descriptor

### Description

Amphiphilic Pseudo Amino Acid Composition Descriptor

### Usage

    extractProtAPAAC(x, props = c("Hydrophobicity", "Hydrophilicity"),
      lambda = 30, w = 0.05, customprops = NULL)

### Arguments

`x` | A character vector, as the input protein sequence.
`props` | A character vector, specifying the properties used. 2 properties are used by default, as listed below: `'Hydrophobicity'` Hydrophobicity value of the 20 amino acids `'Hydrophilicity'` Hydrophilicity value of the 20 amino acids
`lambda` | The lambda parameter for the APAAC descriptors, default is 30.
`w` | The weighting factor, default is 0.05.
`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 Amphiphilic Pseudo Amino Acid Composition (APAAC) descriptor (Dim: `20 + (n * lambda)`, `n` is the number of properties selected, default is 80).

### Value

A length `20 + n * lambda` named vector, `n` is the number of properties selected.

### Note

Note the default `20 * 2` `prop` values have been already independently given in the function. Users could also specify other (up to 544) properties with the Accession Number in the `AAindex` data, with or without the default three properties, which means users should explicitly specify the properties to use.

### Author(s)

Nan Xiao <https://nanx.me>

### References

Kuo-Chen Chou. Prediction of Protein Cellular Attributes Using Pseudo-Amino Acid Composition. PROTEINS: Structure, Function, and Genetics, 2001, 43: 246-255.

Type 2 pseudo amino acid composition. http://www.csbio.sjtu.edu.cn/bioinf/PseAAC/type2.htm

Kuo-Chen Chou. Using Amphiphilic Pseudo Amino Acid Composition to Predict Enzyme Subfamily Classes. Bioinformatics, 2005, 21, 10-19.

JACS, 1962, 84: 4240-4246. (C. Tanford). (The hydrophobicity data)

PNAS, 1981, 78:3824-3828 (T.P.Hopp & K.R.Woods). (The hydrophilicity data)

### See Also

See `extractProtPAAC` for pseudo amino acid composition descriptor.

### Examples

    x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]
    extractProtAPAAC(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 2 default properties, 4 properties in the AAindex database,
    # and 3 cutomized properties
    extractProtAPAAC(x, customprops = myprops,
                     props = c('Hydrophobicity', 'Hydrophilicity',
                               'CIDH920105', 'BHAR880101',
                               'CHAM820101', 'CHAM820102',
                               'MyProp1', 'MyProp2', 'MyProp3'))

[Package Rcpi version 1.20.1 Index]