Bios2cor (version 2.2.1)

write.entropy: 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 = NULL)

Value

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

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. Default is NULL (a "ENTROPY.csv" file is created). If filepathroot is not NULL, a "_ENTROPY.csv" extension is added to the file path root.

Author

Antoine GARNIER

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.

Examples

  #File path for output files
  wd <- tempdir()
  #wd <-getwd() 
  file <- file.path(wd,"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)