This function calculates the Conjoint Triad descriptor, with customized amino acid classification support.
extractCTriadClass(x, aaclass)A length k^3 named vector, where k is the number
of customized classes of the amino acids.
A character vector, as the input protein sequence.
A list containing the customized amino acid classification. See example below.
Nan Xiao <https://nanx.me>
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.
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)
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