Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!
Get Started for Free
Documentation
R
maftools

OncogenicPathways

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

Examples

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

Summarize, Analyze and Visualize MAF Files

v2.6.05
MIT + file LICENSE
Authors
Anand Mayakonda [aut, cre] (<https://orcid.org/0000-0003-1162-687X>)
Initial release
2015-12-14

We don't support your browser anymore

Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.