pssm_composition: PSSM-COMPOSITION feature

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

Description

This feature, which stands for auto covariance transformation, for jth column calculates the average of this column, and then subtracts the resulting number from the elements on the i and (i + g)th rows of this column, and finally multiplies them. by changing the variable i from 1 to L-g, it calculates the sum of these, since the variable j changes between 1 and 20, and the variable g between 1 and 20 eventually a feature vector of length 200 will be obtained.

Usage

pssm_composition(pssm_name)

Arguments

pssm_name

name of PSSM Matrix files

Value

feature vector of length 400

References

L. Zou, C. Nan, and F. J. B. Hu, "Accurate prediction of bacterial type IV secreted effectors using amino acid composition and PSSM profiles," vol. 29, no. 24, pp. 3135-3142, 2013.

Examples

X<-pssm_composition(system.file("extdata", "C7GQS7.txt.pssm", package="PSSMCOOL"))

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