AMP_COAD

A binary matrix, with information about amplifications in Colon Adenocarcinoma, created by applying <code>GDCquery</code> and used as real example in <code>getMutexAB</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

AMP_COAD function

The format is: 
num [1:1000, 1:391] 0 0 0 0 0 0 0 0 0 0 ... 
- attr(*, "dimnames")=List of 2 
..$ : chr [1:1000] "ENSG00000212993.4" "ENSG00000279524.1" "ENSG00000136997.13" "ENSG00000101294.15" ... 
..$ : chr [1:391] "TCGA-CA-6718" "TCGA-D5-6931" "TCGA-AZ-6601" "TCGA-G4-6320" ...

Format

AMP_COAD data — AMP_COAD

AMP_COAD data

AMP_COAD: AMP_COAD data

Description

Usage

Arguments

Format

Examples