fp_hmm: fp_hmm

In protHMM: Protein Feature Extraction from Profile Hidden Markov Models

fp_hmm

Description

This feature consists of two vectors, d, s. Vector d corresponds to the sums across the sequence for each of the 20 amino acid columns. Vector s corresponds to a flattened matrix S[i, j] = \sum_{k = 1}^{L} H[k, j] \times \delta[k, i] in which \delta[k, i] = 1 when A_i = H[k, j]. A refers to a list of all possible amino acids, i, j span from 1:20.

Usage

fp_hmm(hmm)

Arguments

hmm	The name of a profile hidden markov model file.

Value

A vector of length 20.

A vector of length 400.

References

Zahiri, J., Yaghoubi, O., Mohammad-Noori, M., Ebrahimpour, R., & Masoudi-Nejad, A. (2013). PPIevo: Protein–protein interaction prediction from PSSM based evolutionary information. Genomics, 102(4), 237–242.

Examples

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

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