Bios2cor (version 1.2)

delta_weighting: Creation of a Delta weighting filter for each element

Description

Given an entropy object (result of the entropy or of the rotamer_entropyfunction), creates a vector with a delta weighting of each element based on the entropy value. The vector will be used to give different weights to each element in the centered_pca function.

Usage

delta_weighting(entropy, Smin= 0.4, Smax= 0.6)

Arguments

entropy

An object created by the entropy function

Smin

A value indicating the minimum entropy value. (Smin= 0.4 by default)

Smax

A value indicating the maximum entropy value. (Smax= 0.6 by default)

Value

A vecto that contains a weighting score for each element (position in sequence alignment or side chain dihedral angle in trajectory).

Details

The object returned by the entropy or the rotamer_entropy function contains an entropy score for each element. The weighting of each element is calculated as follow : $$ weighting[i] = \left\{ \begin{array}{ll} 1, & Smin < entropy[i] < Smax \\ 0, & otherwise \end{array} \right. $$

Examples

# NOT RUN {
  align <- import.msf(system.file("msa/toy_align.msf", package = "Bios2cor"))

  #Creating ENTROPY object
  entropy <- entropy(align)
  
  filter <- delta_weighting(entropy, Smin= 0.4, Smax= 0.6)
  
# }