pse_pssm: pseudo position-specific scoring matrix feature

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

Description

This feature vector is combination of F_{PSSM} feature vector and vector of correlation factors correspond to 20 columns in PSSM Matrix. F_{PSSM} actually is mean of PSSM Matrix columns of length 20.

Usage

pse_pssm(pssm_name, g = 1)

Arguments

pssm_name	is the name of PSSM matrix file
g	a parameter Which its size corresponds to the database used.

Value

feature vector of length 20+20*g

References

D.-J. Yu et al., "Learning protein multi-view features in complex space," vol. 44, no. 5, pp. 1365-1379, 2013.

Chou, K.C. and Shen, H.B. (2007) MemType-2L: a web server for predicting membrane proteins and their types by incorporating evolution information through Pse-PSSM, Biochemical and Biophysical Research Communications, 360, 339-345.

Examples

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

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