Bios2cor (version 1.2)

shuffle_positions: Amino acids shuffle

Description

Given an alignment object, created by the import.fasta or import.msf function, for each position in the alignment, shuffles the residues at this position to create a random alignment, and calculates the correlation matrix with the selected method.

Usage

shuffle_positions(
    align,
    method,
    fileHelix= NULL,
    gap_val= 0.8,
    z_score= TRUE,
    nb_iterations= 5
  )

Arguments

align

An object created by the import.msf or import.fasta function which requires an alignment file name

method

A string corresponding to selected correlation method. This should be one out of "OMES", "MIP","ELSC" and "MCBASC"

fileHelix

AA file that contains the positions of the anchor residues in the sequence alignment. For use with GPCRs

gap_val

Authorized gap proportion per position. This value can be between 0 and 0.8 (0.8 by default), which means that positions with more than 80 percent of gaps will not be considered

z_score

A logical value to perform a Z-score normalisation of the covariation matrix (TRUE) or not (FALSE). Default is TRUE

nb_iterations

Number of times that alignment must be shuffled. Default is 5

Value

Returns a numeric matrix which is the averaged matrix obtained from re-itering "nb_iterations" times the computation of the correlation matrix from a random alignment with the same composition as the initial alignment

Details

At each position, sequences from the initial alignment will be shuffled to yield a random alignment with the same average composition at each position as the initial alignment and the same sequence entropy profile. The correlation matrix of the resulting alignment will be calculated "nb_iterations" times, then averaged.

Examples

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

  #Shuffling alignment
  corr <- shuffle_positions(align, method="OMES", fileHelix= NULL, gap_val= 0.8, z_score= TRUE,
       nb_iterations= 3)
# }