protr (version 1.4-1)

extractCTriadClass: 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.

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 = "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)
# }