Profile-based protein representation derived by PSSM (Position-Specific Scoring Matrix)

Usage

extractProtPSSMFeature(pssmmat)

Arguments

pssmmat: The PSSM computed by extractProtPSSM.

Value

A numeric vector which has 20 x N named elements, where N is the size of the window (number of rows of the PSSM).

Details

This function calculates the profile-based protein representation derived by PSSM. The feature vector is based on the PSSM computed by extractProtPSSM. For a given sequence, The PSSM feature represents the log-likelihood of the substitution of the 20 types of amino acids at that position in the sequence. Each PSSM feature value in the vector represents the degree of conservation of a given amino acid type. The value is normalized to interval (0, 1) by the transformation 1/(1+e^(-x)).

References

Ye, Xugang, Guoli Wang, and Stephen F. Altschul. "An assessment of substitution scores for protein profile-profile comparison." Bioinformatics 27.24 (2011): 3356--3363.

Rangwala, Huzefa, and George Karypis. "Profile-based direct kernels for remote homology detection and fold recognition." Bioinformatics 21.23 (2005): 4239--4247.

Examples

x = readFASTA(system.file('protseq/P00750.fasta', package = 'Rcpi'))[[1]]
# \donttest{
dbpath = tempfile('tempdb', fileext = '.fasta')
invisible(file.copy(from = system.file('protseq/Plasminogen.fasta', package = 'Rcpi'), to = dbpath))
pssmmat = extractProtPSSM(seq = x, database.path = dbpath)
#> Error in extractProtPSSM(seq = x, database.path = dbpath): Please install makeblastdb (included in the NCBI BLAST+) or specify makeblastdb.path.
pssmfeature = extractProtPSSMFeature(pssmmat)
#> Error in eval(expr, envir, enclos): object 'pssmmat' not found
head(pssmfeature)# }
#> Error in eval(expr, envir, enclos): object 'pssmfeature' not found