dynamic_circular: Circular correlation

In Bios2cor: From Biological Sequences and Simulations to Correlation Analysis

Circular correlation

Description

Calculates circular correlation/covariation scores between side chain dihedral angles during a molecular dynamics trajectory.

Usage

  dynamic_circular(
    dynamic_structure,
    res_selection=
      c("C","I","L","M","V","R","H","K","D","E","N","Q","F","Y","W","T","S","P")
  )

Arguments

dynamic_structure	Object of class 'structure' that is created by the dynamic_structure function
res_selection	List of amino acids that will be taken into account in the correlation/covariation matrix. By default, all the amino acids are taken into account except Gly and Ala, with no side chain dihedral angles.

Details

This function uses the cor.circular function from the circular package based on a circular version of the Pearson coeefficient.

Value

returns a list of four elements which are numeric matrices containing (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).

Author(s)

Bruck TADESSE, Antoine GARNIER, and Marie CHABBERT

References

Circular Statistics, from “Topics in circular Statistics” (2001) S. Rao Jammalamadaka and A. SenGupta, World Scientific.

Examples

  #Reading pdb and dcd files
  pdb <- system.file("rotamer/toy_coordinates.pdb", package= "Bios2cor")
  trj <- system.file("rotamer/toy_dynamics.dcd", package= "Bios2cor")

  #Creating dynamic_structure object for selected frames
  wanted_frames <- seq(from = 1, to = 40, by = 2)
  dynamic_structure <- dynamic_structure(pdb, trj, wanted_frames)

  #Computing circular correlation between dihedral angles of selected residues
  res_selection <- c("H","N","Q","F","Y","W")    
  dihed_corr <- dynamic_circular(dynamic_structure, res_selection)

  #Computing correlation between all dihedral angles 
  #dihed_corr <- dynamic_circular(dynamic_structure)

Bios2cor documentation built on July 8, 2022, 5:05 p.m.