available_rnaseq_workflows {GenomicDataCommons} | R Documentation

## Get RNA-seq quantification from the NCI GDC.

### Description

`gdc_rnaseq` is a high-level function for accessing the NCI GDC RNA-seq data and summarizing as a `SummarizedExperiment`.

### Usage

    available_rnaseq_workflows()

    gdc_rnaseq(project_id, workflow_type)

### Arguments

`project_id` | character() vector with one or more project ids. Available project_ids can be found using `ids(projects())`. Note that not all projects contain RNA-seq data.
`workflow_type` | character(1) with the workflow type. Possible values can be accessed using `available_rnaseq_workflows`

### Details

The RNA-seq data are downloaded using `gdcdata` with caching used as available. The resulting files are read and combined without any transformation. It us up to the user to perform further normalization or transformation if needed.

Clinical information for each file (see `gdc_clinical` for details) is loaded into the `colData` slot. Quality control mapping information is also stored in the `colData` with column names beginning with "qc__".

### Value

a `SummarizedExperiment` object, populated with the expression values, the gene ids in the `rowData`, and the clinical data associated with each sample in the `colData`.

### Functions

- `available_rnaseq_workflows`: Show possible RNA-seq workflow types

### References

See https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/ for details of data processing that occurs at the GDC.

### Examples

    available_rnaseq_workflows()

    ## Not run:
    tcga_se = gdc_rnaseq('TCGA-ACC', 'HTSeq - Counts')
    tcga_se

    ## End(Not run)

[Package GenomicDataCommons version 1.12.0 Index]