write.scores: Creates a correlation/covariation ouput file

In Bios2cor: From Biological Sequences and Simulations to Correlation Analysis

Creates a correlation/covariation ouput file

Description

Given a correlation object, writes the score, the Zscore and, optionally the entropy, for each pair of elements in a csv file.

Usage

  write.scores(correlation, filepathroot, entropy= NULL)

Arguments

correlation	An object created by a correlation/covariation function (omes, mi, mip, elsc, mcbasc, dynamic_circular, dynamic_omes, dynamic_mi, dynamic_mip
entropy	An object created by the entropy function
filepathroot	The root of the full path name for the output file. DEfault is NULL, a "CORR_SCORES.csv" file is created in tempdir(). If not NULL, the "_CORR_SCORES.csv" extension is added to the filepathroot.

Details

Elements represent positions in multiple sequence alignments and side chain dihedral angles in molecular dynamic simulations (MD).

In sequence analysis, the correlation object contains two matrices with the correlation/covariation scores and Z-scores for each pair of elements [i,j]. If entropy = NULL, each line of the output file will contain element i, element j, score[i,j], and Z-score[i,j]. If entropy is not NULL, each line of the output file will contain element i, element j, score[i,j], Zscore[i,j], entropy[i], and entropy[j].

In MD analysis, the correlation object contains four matrices with (1) the correlation/covariation scores for each pair of rotamers (score), (2) the Z-scores for each pair of rotamers (Zscore), (3) the correlation/covariation scores for each pair of rotamers with zero values for autocorrelation (correlation within the same side chain) (score_noauto) and (4) the Z-scores calculated without autocorrelation pairs and zero values for autocorrelation pairs (Zscore_noauto). If entropy = NULL, each line of the output file will contain element i, element j, score[i,j], Zscore[i,j], score_noauto[i,j], and Zscore_noauto[i,j]. If entropy is not NULL, each line of the output file will contain element i, element j, score[i,j], Zscore[i,j], score_noauto[i,j], Zscore_noauto[i,j], entropy[i], and entropy[j].

Value

A csv file containing the correlation/covariation scores and optionally the entropies.

Author(s)

Antoine GARNIER and Marie CHABBERT

Examples

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

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

  #Creating correlation and entropy objects
  correlation <- omes(align, gap_ratio= 0.2)
  entropy <- entropy(align)
  
  #Writing results to csv file
  write.scores(correlation, file, entropy )

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

  #Reading the pdb and dcd files and the angles to rotamers conversion file
  pdb <- system.file("rotamer/toy_coordinates.pdb", package= "Bios2cor")
  trj <- system.file("rotamer/toy_dynamics.dcd", package= "Bios2cor")
  conversion_file <- system.file("rotamer/dynameomics_rotamers.csv", package= "Bios2cor")

  #Creating dynamic_structure and rotamers objects
  wanted_frames <- seq(from = 5, to = 40, by = 10)
  dynamic_structure <- dynamic_structure(pdb, trj, wanted_frames)
  rotamers <- angle2rotamer(dynamic_structure, conversion_file)
  
  #Creating correlation and entropy objects
  wanted_residues <- c("F","H","N","Y","W")
  #dyn_corr <- dynamic_omes(dynamic_structure, rotamers, wanted_residues)
  dyn_corr <- dynamic_circular(dynamic_structure, wanted_residues)
  dyn_entropy <- dynamic_entropy(rotamers)
   
  #Writing results to csv file
  write.scores(dyn_corr, file, dyn_entropy )

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