hmm_bigrams {protHMM}

hmm_bigrams

Description

This feature is calculated with a 20 x 20 matrix B, in which B[i, j] = \sum_{a = 1}^{L-1} H_{a, i}H_{a+1, j}. H corresponds to the original HMM matrix, and L is the number of rows in H. Matrix B is then flattened to a feature vector of length 400, and returned.

Usage

hmm_bigrams(hmm)

Arguments

hmm

The name of a profile hidden markov model file.

Value

A vector of length 400

References

Lyons, J., Dehzangi, A., Heffernan, R., Yang, Y., Zhou, Y., Sharma, A., & Paliwal, K. K. (2015). Advancing the Accuracy of Protein Fold Recognition by Utilizing Profiles From Hidden Markov Models. IEEE Transactions on Nanobioscience, 14(7), 761–772.

Examples

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