hmm_smooth

This feature smooths the HMM matrix \(H\) by using sliding window of length \(sw\) to incorporate information from up and downstream residues into each row of the HMM matrix. Each HMM row \(r_i\) is made into the summation of \(r_{i-(sw/2)}+... r_i...+r_{i+(sw/2)}\), for \(i = 1:L\), where \(L\) is the number of rows in \(H\). For rows such as the beginning and ending rows, \(0\) matrices of dimensions \(sw/2, 20\) are appended to the original matrix \(H\).

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"))