In ashishjain1988/MAFDash: Create an HTML Dashboard to Visualize Data from MAF File

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  echo = TRUE,
  message = FALSE,
  warning = FALSE,
  fig.width=8, fig.height=5
)

Getting started

Installation from Github

# install.packages(devtools)  ## Install devtools if necessary
devtools::install_github("mtandon09/MAFDashRPackage")

Get some mutation data in MAF format

You can run TCGAbiolinks::getGDCprojects() to get a data frame of available datasets. The last column (tumor) contains valid TCGA project codes for download.

library(MAFDash)
library(maftools)
# Let's use the example MAF provided by maftools
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")

Make it into a dashboard

## Text to display as the header in the output file
title_text <- paste0("Example Dashboard")  

## Location for the output file
html_filename <- "LAML.mafdash.html"

getMAFDashboard(maf = laml.maf,
                outputFileName = html_filename,
                outputFileTitle=title_text)

Output

The output can be seen here

ashishjain1988/MAFDash documentation built on Feb. 9, 2023, 9:54 p.m.