write.pca: Creates a file of coordinates in PCA space

In Bios2cor: From Biological Sequences and Simulations to Correlation Analysis

Creates a file of coordinates in PCA space

Description

Given an object of class 'pca' (result of the centered_pca function), stores the coordinates of each element in the PC space in a txt file

Usage

  write.pca(corr_pca,filepathroot, pc=NULL, entropy= NULL)

Arguments

corr_pca	An object created by the centered_pca function from a correlation/covariation matrix
filepathroot	The root for the full path name of the output file where all coordinates on all components are stored. If NULL, a "PCA_COORD.csv" file is created in tempdir(). If not NULL, the "_PCA_COORD.csv extension is added to the filepathroot.
pc	An integer corresponding to the number of principal components for which coordinates of the elements are saved. By default, this number corresponds to the number of components with positive eigen values.
entropy	An object created by the entropy or the dynamic_entropy function. DEfault is NULL.

Details

The object returned by the centered_pca function contains coordinates in the PC space for each element. Each line of the pca file will contain the name of the current element and its coordinates. Any line that contains Na value for X, Y or Z coordinates will be ignored.

Value

returns a file containing the coordinates of each element in PC space.

Author(s)

Antoine GARNIER

Examples

  #File path for output files
  out <- tempdir()
  file <- file.path(out,"test_seq4") 

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

  #Creating OMES correlation object and selecting correlation matrix
  omes <- omes(align, gap_ratio = 0.2)
  omes <-omes$Zscore

  #Creating PCA object for selected matrix
  pca <- centered_pca(omes, filepathroot= file, filter = NULL, pc= NULL, dec_val= 5)
   
  #Saving coordinates of elements in csv file 
  write.pca(pca, file, pc = 10, entropy = NULL)
  

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