maftools (version 0.99.30)

mutExclusive: Performs exact test for mutual exclusive events.

Description

Performs statistical test between given set of genes for mutual excluisiveness.

Usage

mutExclusive(maf, genes = NULL, top = 10)

Arguments

maf

an MAF object generated by read.maf

genes

A pair of genes between which test should be performed. If its null, test will be performed between all combinations of top ten genes.

top

check for exclusiveness among top 'n' number of genes. Defaults to top 10. genes

Value

table with number of events in all possible combinations and p-value. Column header describes mutation status of gene1 and gene2 respectively. n.00 number of samples where both gene1 and gene2 are not mutated c.01 number of samples where gene1 is not mutated but gene2 is mutated and so on.

References

Leiserson, Mark DM et al. CoMEt: A Statistical Approach to Identify Combinations of Mutually Exclusive Alterations in Cancer. Genome Biology 16.1 (2015): 160.

Examples

# NOT RUN {
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf, removeSilent = TRUE, useAll = FALSE)
mutExclusive(maf = laml, top = 5)

# }