tcgaLoad: Loads a TCGA cohort
In PoisonAlien/maftools: Summarize, Analyze and Visualize MAF Files

tcgaLoad

R Documentation

Loads a TCGA cohort

Description

Loads the user mentioned TCGA cohorts

Usage

tcgaLoad(
  study = NULL,
  source = c("MC3", "Firehose"),
  repo = c("github", "gitee")
)

Arguments

`study`	Study names to load. Use `tcgaAvailable` to see available options.
`source`	Source for MAF files. Can be `MC3` or `Firehose`. Default `MC3`. Argument may be abbreviated (M or F)
`repo`	one of "github" (default) and "gitee".

Details

The function loads curated and pre-compiled MAF objects from TCGA cohorts. TCGA data are obtained from two sources namely, Broad Firehose repository, and MC3 project.

Value

An object of class MAF.

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.

Examples

# Loads TCGA LAML cohort (default from MC3 project)
tcgaLoad(study = "LAML")
# Loads TCGA LAML cohort (from Borad Firehose)
tcgaLoad(study = "LAML", source = "Firehose")

PoisonAlien/maftools documentation built on April 7, 2024, 2:49 a.m.