do_cormat: Do a correlation matrix analysis as described by Horvath et...
In nicohuttmann/pOmics: Framework for proteomics data analysis

do_cormat

R Documentation

Do a correlation matrix analysis as described by Horvath et al.

Description

Do a correlation matrix analysis as described by Horvath et al.

Usage

do_cormat(
  data_,
  cor.method = "pearson",
  diag0 = T,
  similarity.method = "none",
  adjacency.method = "none",
  alpha,
  theta,
  beta,
  distance.method = "euclidean",
  clustering.method = "complete",
  dataset,
  plot = T,
  input,
  output = "data_cormat"
)

Arguments

`data_`	list or tibble
`cor.method`	function to compute correlation coefficients
`diag0`	set autocorrelation to 0
`similarity.method`	similarity function ("absolute", "preserve", "none")
`adjacency.method`	adjacency function ("sigmoid", "power", "none")
`alpha`	alpha parameter for sigmoid function
`theta`	theta parameter for sigmoid function
`beta`	beta parameter for power function
`clustering.method`	method to cluster columns and rows ("complete", "average"); see ?hclust for options
`plot`	generate default plot with plot_cor_matrix
`input`	name of input data
`output`	name of output data
`distance.m`	ethod method to calculate distance; see ?dist for options