drugInteractions: Drug-Gene Interactions

In thesushantpatil/maftools: Summarize, Analyze and Visualize MAF Files

Description

Checks for drug-gene interactions and druggable categories

Usage

drugInteractions(
  maf,
  top = 20,
  genes = NULL,
  plotType = "bar",
  drugs = FALSE,
  fontSize = 0.8
)

Arguments

maf	an MAF object generated by read.maf
top	Top number genes to check for. Default 20
genes	Manually specify gene list
plotType	Can be bar, pie Default bar plot.
drugs	Check for known/reported drugs. Default FALSE
fontSize	Default 0.8

Details

This function takes a list of genes and checks for known/reported drug-gene interactions or Druggable categories. All gene-drug interactions and drug claims are compiled from Drug Gene Interaction Databse. See reference for details and cite it if you use this function.

References

Griffith, M., Griffith, O. L., Coffman, A. C., Weible, J. V., McMichael, J. F., Spies, N. C., et. al,. 2013. DGIdb - Mining the druggable genome. Nature Methods.

Examples

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

thesushantpatil/maftools documentation built on May 18, 2020, 9:54 p.m.