extrProtPSSMFeature: Profile-based protein representation derived by PSSM...
In BioMedR: Generating Various Molecular Representations for Chemicals, Proteins, DNAs/RNAs and Their Interactions

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/522-extractProtPSSMFeature.R

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

1	extrProtPSSMFeature(pssmmat)

pssmmat

The PSSM computed by extrProtPSSM.

This function calculates the profile-based protein representation derived by PSSM. The feature vector is based on the PSSM computed by extrProtPSSM. 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)).

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

Min-feng Zhu <wind2zhu@163.com>, Nan Xiao <http://r2s.name>

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.

extrProtPSSM extrProtPSSMAcc

x = readFASTA(system.file('protseq/P00750.fasta', package = 'BioMedR'))[[1]]
dbpath = tempfile('tempdb', fileext = '.fasta')
invisible(file.copy(from = system.file('protseq/Plasminogen.fasta', package = 'BioMedR'), to = dbpath))
pssmmat = extractProtPSSM(seq = x, database.path = dbpath)
pssmfeature = extrProtPSSMFeature(pssmmat)
head(pssmfeature)