fp_hmm {protHMM} | R Documentation |
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"))
[Package protHMM version 0.1.1 Index]