IM_psehmm: IM_psehmm

In protHMM: Protein Feature Extraction from Profile Hidden Markov Models

IM_psehmm

Description

The first twenty numbers of this feature correspond to the means of each column of the HMM matrix H. The rest of the features in the feature vector are found in matrix T[i,j], where T[i,j] = \frac{1}{L-i}\sum_{n = 1}^{20-i} [H_{m,n}-H_{m, n+i}]^2, m = 1:L,\space i = 1:d\space and\space j = 1:20.

Usage

IM_psehmm(hmm, d = 13)

Arguments

hmm	The name of a profile hidden markov model file.
d	The maximum distance between residues column-wise.

Value

A vector of length 20+20\times d-d\times\frac{d+1}{2}

Note

d must be less than 20.

References

Ruan, X., Zhou, D., Nie, R., & Guo, Y. (2020). Predictions of Apoptosis Proteins by Integrating Different Features Based on Improving Pseudo-Position-Specific Scoring Matrix. BioMed Research International, 2020, 1–13.

Examples

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

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