getMutexGroup: getMutexGroup function

In Rediscover: Identify Mutually Exclusive Mutations

getMutexGroup function

Description

Given a binary matrix and its corresponding probability matrix pij, compute the Poisson Binomial method to estimate mutual exclusive events.

Usage

getMutexGroup(A = NULL, PM = NULL, type = "Impurity", lower.tail = TRUE)

Arguments

A	The binary matrix
PM	The corresponding probability matrix of A. It can be computed using function getPM. By default equal to getPM(A)
type	one of Coverage, Exclusivity or Impurity. By default is Impurity
lower.tail	True if mutually exclusive test. False for co-ocurrence. By default is TRUE.

Value

A symmetric matrix with the p.value of the corresponding test.

Examples

  #This first example is a basic 
  #example of how to perform getMutexGroup
  
  data("A_example")
  A2 <- A_example[,1:30]
  A2[1,1:10] <- 1
  A2[2,1:10] <- 0
  A2[3,1:10] <- 0
  A2[1,11:20] <- 0
  A2[2,11:20] <- 1
  A2[3,11:20] <- 0
  A2[1,21:30] <- 0
  A2[2,21:30] <- 0
  A2[3,21:30] <- 1
  PM2 <- getPM(A2)
  A <- A2[1:3,]
  PM <- PM2[1:3,]
  
  getMutexGroup(A, PM, "Impurity")
  getMutexGroup(A, PM, "Coverage")
  getMutexGroup(A, PM, "Exclusivity")
  

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