delta_filter: Creation of an entropy/dynamic score delta filter for each...

In Bios2cor: From Biological Sequences and Simulations to Correlation Analysis

Creation of an entropy/dynamic score delta filter for each element

Description

Given an entropy object (result of the entropy or of the dynamic_entropy function), creates a vector with a delta filter of each element based on the entropy value. The vector will be used to limit the analysis to the elements in the given entropy range in the centered_pca and top_pairs_analysis functions.

Usage

  delta_filter(entropy, Smin = 0, Smax = 1)

Arguments

entropy	An object created by the entropy or the dynamic_entropyfunction
Smin	A value indicating the minimum entropy value. (Smin = 0 by default)
Smax	A value indicating the maximum entropy value. (Smax = 1 by default)

Details

The object returned by the entropy or the dynamic_entropy function contains an entropy score for each element. The delta weighting of each element is calculated as follow :

weighting[i] = \left\{ \begin{array}{ll} 1, & Smin < entropy[i] < Smax \\ 0, & otherwise \end{array} \right.

Value

A vector that contains a 0 or 1 weighting score for each element (position in sequence alignment or side chain dihedral angle in trajectory) to limit principal component and top pair analysis to elements within a given entropy range.

Author(s)

Antoine GARNIER

Examples

  #Importing MSA
  align <- import.msf(system.file("msa/toy_align.msf", package = "Bios2cor"))

  #Creating entropy object
  entropy <- entropy(align)
  
  #Creating delta filter based on entropy
  filter <- delta_filter(entropy, Smin = 0.4, Smax = 0.6)
  

Bios2cor documentation built on April 4, 2025, 4:14 a.m.