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