Bios2cor (version 1.2)

create_corrfile: Creates a correlation file

Description

Given a correlation object, stores the correlation score of each pair of elements in a txt file.

Usage

create_corrfile(corr_struct, entropy= NULL, auto_pairing= FALSE, filepath)

Arguments

corr_struct

An object created by a correlation function (omes, mip, elsc, mcbasc, rotamer_circular, rotamer_omes, rotamer_mip

entropy

An object created by the entropy function

auto_pairing

Option that allows/removes correlation scores between dihedral angles of the same residue in the correlation matrix (valid only for side chain correlations in molecular simulations)

filepath

The full path name of the output file

Value

A txt file containing the correlation scores and optionally the entropies

Details

The correlation structure contains a score for each pair of elements [i,j]. Elements represent positions in the sequence alignments and side chain dihedral angles in molecular simulations. If entropy = NULL, each line of the correlation file will contain element i, element j and score [i,j]. If entropy is not NULL, each line of the correlation file will contain element i, element j, entropy[i], entropy[j] and score [i,j]

Examples

# NOT RUN {
  msf <- system.file("msa/toy_align.msf", package = "Bios2cor")
  align <- import.msf(msf)

  #Creating OMES object
  omes <- omes(align,fileHelix= NULL , diag= 0, fileCSV= NULL, gap_val= 0.8, z_score= TRUE)
  omes <-omes$normalized
  
  create_corrfile(omes, entropy= NULL, auto_pairing= FALSE, "corr_results.txt")
# }