tcgaLoad {maftools} | 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.

### See Also

`tcgaAvailable`

### Examples

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

[Package maftools version 2.10.05 Index]