oncoPrintTCGA: OncoPrint for TCGA Mutation Assays

Description Usage Arguments Value Examples

View source: R/oncoPrintTCGA.R

Description

OncoPrint for TCGA Mutation Assays

Usage

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

Arguments

multiassayexperiment

A MultiAssayExperiment preferably 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

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library(curatedTCGAData)

acc <- curatedTCGAData("ACC", "Mutation", FALSE)

oncoPrintTCGA(acc)

TCGAutils documentation built on April 17, 2021, 6:04 p.m.