OncogenicPathways {maftools} | R Documentation

## Enrichment of known oncogenic pathways

### Description

Checks for enrichment of known oncogenic pathways

### Usage

    OncogenicPathways(maf, pathways = NULL, fontSize = 1, panelWidths = c(2, 4, 4))

### Arguments

`maf` | an `MAF` object generated by `read.maf`
`pathways` | Can be a two column data.frame/tsv-file with pathway-name and genes involved in them. Default 'NULL', uses a predefined list of pathways. See reference for details.
`fontSize` | Default 1
`panelWidths` | Default c(2, 4, 4)

### Details

Oncogenic signalling pathways are derived from TCGA cohorts. See reference for details.

### Value

Prints fraction of altered pathway

### References

Sanchez-Vega F, Mina M, Armenia J, Chatila WK, Luna A, La KC, Dimitriadoy S, Liu DL, Kantheti HS, Saghafinia S et al. 2018. Oncogenic Signaling Pathways in The Cancer Genome Atlas. Cell 173: 321-337 e310

### See Also

`PlotOncogenicPathways`

### Examples

    laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
    laml <- read.maf(maf = laml.maf)
    OncogenicPathways(maf = laml)

[Package maftools version 2.10.05 Index]