write.entropy: Writes and displays entropy values

In Bios2cor: From Biological Sequences and Simulations to Correlation Analysis

Writes and displays entropy values

Description

Given an entropy/dynamic_entropy object, writes each element (position or dihedral angle) and its entropy/dynamic_entropy value in a csv file, and displays the histogram.

Usage

  write.entropy(entropy, filepathroot )

Arguments

entropy	An object created by the entropy or the dynamic_entropy function.
filepathroot	The root of the full path name for the entropy output file. If NULL, a "ENTROPY.csv" file is created in tempdir(). If not NULL, a "_ENTROPY.csv" extension is added to filepathroot.

Details

The entropy function calculates entropy score for each position of an alignment file. The dynamic_entropyfunction calculate a "dynamic entropy" score for each side chain dihedral angle of a protein during a molecular simulations.

Value

A csv file containing the elements and their scores. A png file displaying the histogram of the scores.

Author(s)

Antoine GARNIER

Examples

  #File path for output files
  out <- tempdir()
  file <- file.path(out,"test_seq") 

  #Importing multiple sequence alignment
  align <- import.msf(system.file("msa/human_gpcr.msf", package = "Bios2cor"))

  #Creating entropy object
  entropy <- entropy(align, gap_ratio = 0.2)
  
  #Writing results to csv file
  write.entropy(entropy, file)

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