extrPCMBLOSUM: Generalized BLOSUM and PAM Matrix-Derived Descriptors

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

Description

Generalized BLOSUM and PAM Matrix-Derived Descriptors

Usage

extrPCMBLOSUM(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, AAPAM250. Default is 'AABLOSUM62'.
k	Integer. The number of selected scales (i.e. the first k scales) derived by the substitution matrix. This could 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.

Details

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

Value

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

Author(s)

Min-feng Zhu <[e-mail]>, Nan Xiao <http://r2s.name>

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 = 'BioMedR'))[[1]]
blosum = extrPCMBLOSUM(x, submat = 'AABLOSUM62', k = 5, lag = 7, scale = TRUE, silent = FALSE)

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