hmm_smooth {protHMM} | R Documentation |
hmm_smooth
Description
This feature smooths the HMM matrix by using sliding window of length
to incorporate information
from up and downstream residues into each row of the HMM matrix. Each HMM row
is made into the summation
of
, for
, where
is the number of rows in
.
For rows such as the beginning and ending rows,
matrices of dimensions
are appended to the
original matrix
.
Usage
hmm_smooth(hmm, sw = 7)
Arguments
hmm |
The name of a profile hidden markov model file. |
sw |
The size of the sliding window. |
Value
A matrix of dimensions L 20.
References
Fang, C., Noguchi, T., & Yamana, H. (2013). SCPSSMpred: A General Sequence-based Method for Ligand-binding Site Prediction. IPSJ Transactions on Bioinformatics, 6(0), 35–42.
Examples
h<- hmm_smooth(system.file("extdata", "1DLHA2-7", package="protHMM"))
[Package protHMM version 0.1.1 Index]