hmm_smooth {protHMM}R Documentation

hmm_smooth

Description

This feature smooths the HMM matrix HH by using sliding window of length swsw to incorporate information from up and downstream residues into each row of the HMM matrix. Each HMM row rir_i is made into the summation of ri(sw/2)+...ri...+ri+(sw/2)r_{i-(sw/2)}+... r_i...+r_{i+(sw/2)}, for i=1:Li = 1:L, where LL is the number of rows in HH. For rows such as the beginning and ending rows, 00 matrices of dimensions sw/2,20sw/2, 20 are appended to the original matrix HH.

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 ×\times 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]