R/420-extractPCMBLOSUM.R
extractPCMBLOSUM.Rd
Generalized BLOSUM and PAM Matrix-Derived Descriptors
extractPCMBLOSUM(x, submat = "AABLOSUM62", k, lag, scale = TRUE, silent = TRUE)
x | A character vector, as the input protein sequence. |
---|---|
submat | Substitution matrix for the 20 amino acids. Should be one of
|
k | Integer. The number of selected scales (i.e. the first
|
lag | The lag parameter. Must be less than the amino acids. |
scale | Logical. Should we auto-scale the substitution matrix
( |
silent | Logical. Whether we print the relative importance of
each scales (diagnal value of the eigen decomposition result matrix B)
or not.
Default is |
A length lag * p^2
named vector,
p
is the number of scales selected.
This function calculates the generalized BLOSUM matrix-derived descriptors.
For users' convenience, Rcpi
provides the
BLOSUM45, BLOSUM50, BLOSUM62, BLOSUM80, BLOSUM100,
PAM30, PAM40, PAM70, PAM120, and PAM250 matrices
for the 20 amino acids to select.
Georgiev, A. G. (2009). Interpretable numerical descriptors of amino acid space. Journal of Computational Biology, 16(5), 703--723.
# NOT RUN { x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]] blosum = extractPCMBLOSUM(x, submat = 'AABLOSUM62', k = 5, lag = 7, scale = TRUE, silent = FALSE) # }