extractCTriadClass: Conjoint Triad Descriptor (with customized amino acid...

In protr: Generating Various Numerical Representation Schemes for Protein Sequences

Conjoint Triad Descriptor (with customized amino acid classification support)

Description

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

Usage

extractCTriadClass(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.

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)

Nan Xiao <https://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 = "protr"))[[1]]

# use 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")
)

extractCTriadClass(x, aaclass = newclass)

protr documentation built on Sept. 12, 2024, 6:44 a.m.