smoothed_PSSM: smoothed PSSM feature

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

Description

In this function at first a Matrix called smoothed-PSSM is constructed from PSSM Matrix by applying "ws" parameter which called sliding window size and taken from user and usually is equals to 7. Then using other window size parameter "w" which usually equals to 11 at each position smoothed feature vector is constructed.

Usage

smoothed_PSSM(pssm_name, ws = 7, w = 50, v = NULL)

Arguments

pssm_name	name of PSSM Matrix file
ws	window size for smoothing PSSM Matrix
w	window size for extracting feature vector
v	vector of desired positions to extract their features

Details

In the construction of a smoothed PSSM, each row vector of a residue α_i is represented and smoothed by the summation of ws surrounding row vectors (V_{smoothed_i}=V_{i-(ws-1)/2}+...+V_i+...+ V_{i+(ws+1)/2}) For the N-terminal and C-terminal of a protein, (w-1)/2 ZERO vectors, are appended to the head or tail of a smoothed PSSM profile. Using the smoothed PSSM encoding scheme the feature vector of a residue α_i is represented by (V_{smoothed_i-(ws-1)/2},...,V_{smoothed_i},...,V_{smoothed_i+(ws+1)/2}) The feature values in each vector are normalized to a range between -1 and 1.

Value

a matrix of feature vectors

References

Cheng, C.W., et al. (2008) Predicting RNA-binding sites of proteins using support vector machines and evolutionary information, BMC Bioinformatics, 9 Suppl 12, S6.

See Also

kiderafactor

Examples

X<-smoothed_PSSM(system.file("extdata", "C7GQS7.txt.pssm", package="PSSMCOOL"),7,11,c(2,3,8,9))

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