extractBLOSUM: BLOSUM and PAM Matrix-Derived Descriptors

In protr: Generating Various Numerical Representation Schemes for Protein Sequences

BLOSUM and PAM Matrix-Derived Descriptors

Description

This function calculates BLOSUM matrix-derived descriptors. For users' convenience, protr provides the BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM100, PAM30, PAM40, PAM70, PAM120, and PAM250 matrices for the 20 amino acids to select from.

Usage

extractBLOSUM(x, submat = "AABLOSUM62", k, lag, scale = TRUE, silent = TRUE)

Arguments

x	A character vector, as the input protein sequence.
submat	Substitution matrix for the 20 amino acids. Should be one of AABLOSUM45, AABLOSUM50, AABLOSUM62, AABLOSUM80, AABLOSUM100, AAPAM30, AAPAM40, AAPAM70, AAPAM120, or AAPAM250. Default is "AABLOSUM62".
k	Integer. The number of selected scales (i.e. the first k scales) derived by the substitution matrix. This can be selected according to the printed relative importance values.
lag	The lag parameter. Must be less than the amino acids.
scale	Logical. Should we auto-scale the substitution matrix (submat) before doing eigen decomposition? Default is TRUE.
silent	Logical. Whether we print the relative importance of each scales (diagnal value of the eigen decomposition result matrix B) or not. Default is TRUE.

Value

A length lag * p^2 named vector, p is the number of scales selected.

Author(s)

Nan Xiao <https://nanx.me>

References

Georgiev, A. G. (2009). Interpretable numerical descriptors of amino acid space. Journal of Computational Biology, 16(5), 703–723.

Examples

x <- readFASTA(system.file("protseq/P00750.fasta", package = "protr"))[[1]]
blosum <- extractBLOSUM(x, submat = "AABLOSUM62", k = 5, lag = 7, scale = TRUE, silent = FALSE)

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