getPM: getPM function

In Rediscover: Identify Mutually Exclusive Mutations

getPM function

Description

Given a binary matrix estimates the corresponding probability matrix pij.

Usage

getPM(A)

Arguments

A	The binary matrix

Value

A 'PMatrix' object with the corresponding probability estimations. This 'PMatrix' object stored the corresponding coefficients of the logistic regression computed. With this coefficients it is possible to build the complete matrix of probabilities.

Examples

  #This first example is a basic example of how to perform getPM: 
  
  data("A_example")
  PMA <- getPM(A_example)
  
  #The next example, is the same as the first one but, 
  #using a matrix of class Matrix: 
  
  data("A_Matrix")
  PMA_Matrix <- getPM(A_Matrix)
  
  ## Not run: 
  #Finally, the last example, shows a real example 
  #of how to perform this function when when using
  #data from TCGA, Colon Adenocarcinoma in this case: 
  data("TCGA_COAD")
  PM_COAD <- getPM(TCGA_COAD)
  
## End(Not run)

Rediscover documentation built on April 14, 2023, 5:14 p.m.