TCGAvisualize_mutation

A data frame with the cluters and subytpe of cancers

data

colors

samples

geneList

Name of the file to save the plot, can be pdf, png, svg etc..

filename

plot only if number of mutated genes are higher than threshold

threshold

type of plot. Options: "genes" and "cluster".
 By "genes" the axis will receive the genes
and how many samples are mutated. By "cluster" will show the mutations of
only one gene in the cluster.

Must be provided if by is set to "cluster"

groupCol

na.rm

The aim of TCGAbiolinks is : i) facilitate the TCGA open-access
data retrieval, ii) prepare the data using the appropriate pre-processing
strategies, iii) provide the means to carry out different standard analyses
and iv) allow the user to download a specific version of the data and thus
to easily reproduce earlier research results. In more detail, the package
provides multiple methods for analysis (e.g., differential expression analysis,
identifying differentially methylated regions) and methods for visualization
(e.g., survival plots, volcano plots, starburst plots) in order to easily
develop complete analysis pipelines.

TCGAvisualize_mutation: Visualize mutation

Description

Usage

Arguments

Value