oncoPrintTCGA: OncoPrint for TCGA Mutation Assays

In waldronlab/TCGAutils: TCGA utility functions for data management

OncoPrint for TCGA Mutation Assays

Description

OncoPrint for TCGA Mutation Assays

Usage

oncoPrintTCGA(
  multiassayexperiment,
  matchassay = "*_Mutation-*",
  variantCol = "Variant_Classification",
  brewerPal = "Set3",
  ntop = 25,
  incl.thresh = 0.01,
  rowcol = "Hugo_Symbol"
)

Arguments

multiassayexperiment	A MultiAssayExperiment, usually from curatedTCGAData
matchassay	character(1) The name of the assay containing mutation data, this can be a pattern (e.g., "_Mutation-", the default)
variantCol	character(1) The name of the metadata column containing the mutation categories, usually "Variant_Classification" in TCGA
brewerPal	character(1) The name of the RColorBrewer::brewer.pal palette, (default: "Set3")
ntop	integer(1) The number of the top N genes for displaying based on per-sample mutation frequency
incl.thresh	double(1) The inclusion threshold for empirical mutations, mutations less frequent than this value will not be included
rowcol	character(1) The name of the column in the metadata to annotate the rows with either "Hugo_Symbol" (default) or

Value

An oncoPrint plot of mutations

Examples

library(curatedTCGAData)

acc <- curatedTCGAData("ACC", "Mutation", version = "1.1.38", FALSE)

oncoPrintTCGA(acc)

waldronlab/TCGAutils documentation built on Dec. 19, 2024, 2:11 p.m.