OncogenicPathways {maftools}R Documentation

Enrichment of known oncogenic pathways

Description

Checks for enrichment of known oncogenic pathways

Usage

OncogenicPathways(maf)

Arguments

maf

an MAF object generated by read.maf

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 2.2.10 Index]