TCGA_COAD

A binary matrix, with information about genes mutations in Colon Adenocarcinoma, created by applying <code>maftools</code> to .maf file and used as real example in <code>getPM</code> and <code>getMutex</code> and <code>getMutexAB</code> and <code>getMutexGroup</code>.

datasets

An optimized method for identifying mutually
exclusive genomic events. Its main contribution is a
statistical analysis based on the Poisson-Binomial
distribution that takes into account that some samples
are more mutated than others. See [Canisius, Sander, John WM Martens,
and Lodewyk FA Wessels. (2016) "A novel independence test for
somatic alterations in cancer shows that
biology drives mutual exclusivity but chance explains
most co-occurrence." Genome biology 17.1 : 1-17. <doi:10.1186/s13059-016-1114-x>].
The mutations matrices are sparse matrices. The method developed takes
advantage of the advantages of this type of matrix to save
time and computing resources.

Juan A. Ferrer-Bonsoms Developer

Rediscover

Identify Mutually Exclusive Mutations

Juan A. Ferrer-Bonsoms

Laura Jareno

Angel Rubio

TCGA_COAD function

The format is: 
num [1:399, 1:17616] 1 1 1 1 1 1 1 1 1 1 ... 
- attr(*, "dimnames")=List of 2 
..$ : chr [1:399] "TCGA-CA-6718" "TCGA-D5-6931" "TCGA-AZ-6601" "TCGA-G4-6320" ... 
..$ : chr [1:17616] "APC" "TP53" "TTN" "KRAS" ...

TCGA_COAD: TCGA_COAD

Description

Usage

Arguments

Format

Examples