RPM_PSSM: RPM-PSSM feature vector

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

Description

In this feature The idea is similar to the probe concept used in microarray technologies, where probes are used to identify genes. For the convenience, we call it residue probing method. In our application, each probe is an amino acid, which corresponds to a particular column in the PSSM profiles. For each probe, we average the PSSM scores of all the amino acids in the associated column with a PSSM value greater than zero in the sequence, which leads to a 1 20 feature vector. Once again, for the 20 probes, the final feature for each protein sequence is a 1 400 vector.

Usage

RPM_PSSM(pssm_name)

Arguments

pssm_name

name of PSSM Matrix file

Value

RPM-PSSM feature vector of length 400

References

Jeong, J.C., Lin, X. and Chen, X.W. (2011) On position-specific scoring matrix for protein function prediction , IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM, 8, 308-315.

Examples

X<- RPM_PSSM(system.file("extdata","C7GRQ3.txt.pssm",package="PSSMCOOL"))

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