add_metadata {recount} | R Documentation

## Add additional curated metadata to a recount rse object

### Description

This function appends sample metadata information to a RangedSummarizedExperiment-class from the recount2 project. The sample metadata comes from curated efforts independent from the original recount2 project. Currently the only information comes from the recount_brain project described in more detail at http://lieberinstitute.github.io/recount-brain/.

### Usage

    add_metadata(rse, source = "recount_brain_v2", is_tcga = FALSE,
      verbose = TRUE)

### Arguments

`rse` | A RangedSummarizedExperiment-class object as downloaded with download_study. If this argument is not specified, the function will return the raw metadata table.
`source` | A valid source name. The only supported options at this moment are `recount_brain_v1` and `recount_brain_v2`.
`is_tcga` | Set to `TRUE` only when `rse` is from TCGA. Otherwise set to `FALSE` (default).
`verbose` | If `TRUE` it will print a message of where the predictions file is being downloaded to.

### Details

For `source = "recount_brain_v1"` and `source = "recount_brain_v2"`, the metadata columns are described at http://lieberinstitute.github.io/recount-brain/. Alternatively, you can explore `recount_brain_v2` interactively at https://jhubiostatistics.shinyapps.io/recount-brain/.

If you use the recount_brain data please cite the Razmara et al. bioRxiv, 2019 https://www.biorxiv.org/content/10.1101/618025v1. A bib file is available via citation('recount').

### Value

A RangedSummarizedExperiment-class object with the sample metadata columns appended to the `colData()` slot.

### Author(s)

Leonardo Collado-Torres

### References

Razmara et al, bioRxiv, 2019. https://www.biorxiv.org/content/10.1101/618025v1

### Examples

    ## Add the sample metadata to an example rse_gene object
    rse_gene <- add_metadata(rse_gene_SRP009615, 'recount_brain_v2')

    ## Explore the metadata
    colData(rse_gene)

    ## For a list of studies present in recount_brain check
    ## http://lieberinstitute.github.io/recount-brain/.
    ## recount_brain_v2 includes GTEx and TCGA brain samples in addition to the
    ## recount_brain_v1 data, plus ontology information.

    ## Obtain all the recount_brain_v2 metadata if you want to
    ## explore the metadata manually
    recount_brain_v2 <- add_metadata(source = 'recount_brain_v2')

[Package recount version 1.12.1 Index]