extrProtCTriadClass: Conjoint Triad Descriptor (with Customized Amino Acid...

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

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.

Details

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

Value

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

Note

For this descriptor type, users need to intelligently evaluate the underlying details of the descriptors provided, instead of using this function with their data blindly. It would be wise to use some negative and positive control comparisons where relevant to help guide interpretation of the results.

Author(s)

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

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

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)

BioMedR documentation built on Nov. 17, 2017, 10:08 a.m.