/TCGAmutations

R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)

Primary LanguageRMIT LicenseMIT

TCGAmutations - An R data package for TCGA somatic mutations

Introduction

TCGAmutations is an R data package containing somatic mutations from TCGA cohorts. This is particularly useful for those working with mutation data from TCGA studies - where most of the time is spent on searching various databases, downloading, compiling and tidying up the data before even the actual analysis is started. This package tries to mitigate the issue by providing pre-compiled, curated somatic mutations from 33 TCGA cohorts along with relevant clinical information for all sequenced samples.

Data source

There are two sources from which MAF files were compiled:

Installation

devtools::install_github(repo = "PoisonAlien/TCGAmutations")

Requirements

Only dependency is Bioconductor package maftools and all TCGA cohorts are stored as MAF objects. You can install stable version of maftools package from Bioconductor if you do not have it installed already.

source("https://bioconductor.org/biocLite.R")
biocLite("maftools")

Or you can install it from GitHub for developmental version.

devtools::install_github(repo = "PoisonAlien/maftools")

References

Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines Kyle Ellrott, Matthew H. Bailey, Gordon Saksena, et. al. Cell Syst. 2018 Mar 28; 6(3): 271–281.e7. https://doi.org/10.1016/j.cels.2018.03.002