extrProtAPAAC: Amphiphilic Pseudo Amino Acid Composition Descriptor

In wind22zhu/BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs, RNAs and Their Interactions

Description

Amphiphilic Pseudo Amino Acid Composition Descriptor

Usage

extrProtAPAAC(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)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

References

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

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 extrProtPAAC for pseudo amino acid composition descriptor.

Examples

x = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]
extrProtAPAAC(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
extrProtAPAAC(x, customprops = myprops,
                 props = c('Hydrophobicity', 'Hydrophilicity',
                           'CIDH920105', 'BHAR880101',
                           'CHAM820101', 'CHAM820102',
                           'MyProp1', 'MyProp2', 'MyProp3'))

wind22zhu/BioMedR documentation built on Oct. 21, 2019, 12:51 p.m.