Calculates a score for each pair of residus in the sequenec alignment. It relies on a substitution matrix giving a similarity score for each pair of amino acids.
mcbasc(align, fileHelix= NULL, diag= 0, fileCSV= NULL, gap_val= 0.8, z_score= TRUE)An object of class 'align' created by the import.msf or the import.fasta function from a sequence alignment
A string of characters that indicates the file containing the positions of the anchor residues in the sequence alignment. To be used for the analysis of GPCR sequences. Default is NULL.
A numeric value indicating the score of the diagonal elements in the scoring matrix. Default is 0.
A string of characters indicating the name of the csv file where the output matrix will be saved. Default is NULL.
Numeric value indicating the gap ratio at a given position for this position to be taken into account. This value must be between 0 and 0.8. Default is 0.8, which means that positions with more than 80 percent of gaps will not be taken into account.
A boolean for Z-score normalisation of the covariation matrix. Default is TRUE.
A list of two elements : a matrix containing a correlation score for each pair of rotamer and its normalized version
The McBASC score at position [i,j] has been computed with a formula which was initially proposed by Valencia and coworkers(1) as follow :
$${McBASC(i,j)} = \frac{1}{N^2\sigma(i)\sigma(j)} \sum_{k,l}^{ } (SC_{k,l}(i)-SC(i))(SC_{k,l}(j)-SC(j))$$
where :
\(SC_{k,l}(i)\) is the score for the amino acid pair present in sequences k and l at position i
\(SC_{k,l}(j)\) is the score for the amino acid pair present in sequences k and l at position j
\(SC(i)\) is the average of all the scores \(SC_{k,l}(i)\)
\(SC(j)\) is the average of all the scores \(SC_{k,l}(j)\)
\(\sigma(i)\) is the standard deviation of all the scores \(SC_{k,l}(i)\)
\(\sigma(j)\) is the standard deviation of all the scores \(SC_{k,l}(j)\)
(1) Gobel U, Sander C, Schneider R, Valencia A. Correlated mutations and residue contacts in proteins. Proteins 1994;18:309-317.
# NOT RUN {
align <- import.msf(system.file("msa/toy_align.msf", package = "Bios2cor"))
#Creating McBASC object
mcbasc <- mcbasc(align)
# }
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