fp_hmm {protHMM}R Documentation

fp_hmm

Description

This feature consists of two vectors, d,sd, s. Vector dd corresponds to the sums across the sequence for each of the 20 amino acid columns. Vector ss corresponds to a flattened matrix S[i,j]=k=1LH[k,j]×δ[k,i]S[i, j] = \sum_{k = 1}^{L} H[k, j] \times \delta[k, i] in which δ[k,i]=1\delta[k, i] = 1 when Ai=H[k,j]A_i = H[k, j]. AA refers to a list of all possible amino acids, i,ji, j span from 1:201:20.

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"))


[Package protHMM version 0.1.1 Index]