oncoprint: Oncoprint plots

In brightchan/cjbmisc:

Description

A group of functions for oncoprint plots using simplied single functions.

• maf2oncoprintdf: Input a maf, generate the dataframe of gene mutation types for each patients as the input for oncoprint plot.

Usage

maf2oncoprintdf(
  inpmaf,
  gene = NULL,
  ordergene = FALSE,
  coding = TRUE,
  noSilent = FALSE,
  mergeVariant = TRUE,
  subtypeOrder = NULL
)

Arguments

inpmaf	dataframe of the input maf, should have the columns of Variant_Classification, Hugo_Symbol, and Tumor_Sample_Barcode
gene	vector of characters for the symbols of genes to be plotted. Default all genes.
ordergene	boolean for whether the genes should be orderd by the order of the gene list
coding	boolean for whether to subset only the coding mutations
noSilent	boolean for whether to remove the silent mutations
mergeVariant	boolean for whether to merge the "Del and Ins" to "Indel" and various mutations to "Translation_Start_Site"
subtypeOrder	a cha vector specifying the subtype of the samples, the oncodf will be ordered by subtype first.

Value

a plot saved in desinated path

See Also

oncoPrint

brightchan/cjbmisc documentation built on Nov. 5, 2021, 4:12 p.m.