kiderafactor: kiderafactor feature

In PSSMCOOL: Features Extracted from Position Specific Scoring Matrix (PSSM)

Description

For product of this feature vector similar to smoothed_PSSM feature, firstly PSSM Matrix is smoothed by appending zero vectors to its head and tail and utilizing sliding window of size odd, then this smoothed PSSM Matrix is condensed by the Kidera factors to produce feature vector for each residue.

Usage

kiderafactor(pssm_name, v = NULL)

Arguments

pssm_name	name of PSSM Matrix file
v	vector of amino acids positions which we want to produce feature vector for them.

Value

matrix of feature vectors

References

C. Fang, T. Noguchi, H. J. I. j. o. d. m. Yamana, and bioinformatics, "Condensing position-specific scoring matrixs by the Kidera factors for ligand-binding site prediction," vol. 12, no. 1, pp. 70-84, 2015.

See Also

smoothed_PSSM

Examples

X<-kiderafactor(system.file("extdata", "C7GQS7.txt.pssm", package="PSSMCOOL"),c(2,3,8,9))

PSSMCOOL documentation built on Jan. 4, 2022, 5:07 p.m.