hmm_Single_Average: hmm_Single_Average

In protHMM: Protein Feature Extraction from Profile Hidden Markov Models

hmm_Single_Average

Description

This feature groups together rows that are related to the same amino acid. This is done using a vector SA(k), in which k spans 1:400 and SA(k) = avg_{i = 1, 2... L}H[i, j] \times \delta(P(i), A(z)), in which H is the HMM matrix, P in the protein sequence, A is an ordered set of amino acids, the variables j, z = 1:20, the variable k = j + 20 \times (z-1) when creating the vector, and \delta() represents Kronecker's delta.

Usage

hmm_Single_Average(hmm)

Arguments

hmm	The name of a profile hidden markov model file.

Value

A vector of length 400.

References

Nanni, L., Lumini, A., & Brahnam, S. (2014). An Empirical Study of Different Approaches for Protein Classification. The Scientific World Journal, 2014, 1–17.

Examples

h<- hmm_Single_Average(system.file("extdata", "1DLHA2-7", package="protHMM"))

protHMM documentation built on July 9, 2023, 6:10 p.m.