# Introduction to Rediscover

We present *Rediscover*, an R package to identify mutually
exclusive genomic events. It reimplements a privious R package
(*Discover*) whose main contribution is a statistical analysis
based on the Poisson-Binomial distribution that takes into account that
some samples are more mutated than others. *Rediscover* is much
faster than the
discover
implementation.

## Installation

Rediscover can be installed from CRAN repository:

`install.packages("Rediscover")`

## Introduction

The package library has two main parts:

- Estimation of the probabilities \(p_
{ij}\) that gene
*i* is mutated in sample *j*
-assuming conditional independence between genes and samples-.
- Estimation of p-values using the Poisson-Binomial distribution,
using the previous probabilities and the number of samples in which two
genes are co-mutated. The corresponding null hypothesis \(H_0\) is that the mutational status of both
genes is independent of each other.

The second step is the estimation of the p-values using these
probabilities and the number of samples where two genes are co-altered.
*Rediscover* offers different functions depending on the desired
study:

`getMutex`

if the user wants to evaluate
if genes are mutually exclusive.
`getMutexAB`

if the user wants to
evaluate if genes are mutually exclusive with respect to another event
(amplifications, deletions, etcâ€¦)
`getMutexGroup`

will be used when the
user wants to obtain the probability that a certain group of genes being
mutually exclusive. Unlike the `getMutex`

function, in this
case the users introduces the set of genes of interest.

*Rediscover* also provides a function to integrate its usage
with
`maftools`

and
`TCGAbiolinks`

.
Specifically, we added to the function `somaticInteractions`

from `maftools`

our analyses based on the Poisson-Binomial
distribution resulting in a new function called
`discoversomaticInteractions`

.