BioMedR (version 1.2.1)

extrProtCTriadClass: Conjoint Triad Descriptor (with Customized Amino Acid Classification Support)

Description

Conjoint Triad Descriptor (with Customized Amino Acid Classification Support)

Usage

extrProtCTriadClass(x, aaclass)

Arguments

x

A character vector, as the input protein sequence.

aaclass

A list containing the customized amino acid classification. See example below.

Value

A length k^3 named vector, where k is the number of customized classes of the amino acids.

Details

This function calculates the Conjoint Triad descriptor, with customized amino acid classification support.

References

J.W. Shen, J. Zhang, X.M. Luo, W.L. Zhu, K.Q. Yu, K.X. Chen, Y.X. Li, H.L. Jiang. Predicting Protein-protein Interactions Based Only on Sequences Information. Proceedings of the National Academy of Sciences. 007, 104, 4337--4341.

Examples

# NOT RUN {
x = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]

# using customized amino acid classification (normalized van der Waals volume)
newclass = list(c('G', 'A', 'S', 'T', 'P', 'D', 'C'),
                c('N', 'V', 'E', 'Q', 'I', 'L'),
                c('M', 'H', 'K', 'F', 'R', 'Y', 'W'))

extrProtCTriadClass(x, aaclass = newclass)
# }