oncoPrintTCGA {TCGAutils} | R Documentation |
OncoPrint for TCGA Mutation Assays
oncoPrintTCGA( multiassayexperiment, matchassay = "*_Mutation-*", variantCol = "Variant_Classification", brewerPal = "Set3", ntop = 25, incl.thresh = 0.01, rowcol = "Hugo_Symbol" )
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 |
An oncoPrint plot of mutations
library(curatedTCGAData) acc <- curatedTCGAData("ACC", "Mutation", version = "1.1.38", FALSE) oncoPrintTCGA(acc)