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_v1", 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

If you use the recount_brain data please cite the Razmara et al bioRxiv pre-print available at (TODO update URL once it's available). See citation details with citation('recount').

### Value

A RangedSummarizedExperiment-class object with the sample metadata columns appended to the `colData()` slot. For `source = "recount_brain_v1"`, the metadata columns are described at http://lieberinstitute.github.io/recount-brain/. For `source = "recount_brain_v2"`, the metadata columns are described at http://lieberinstitute.github.io/recount-brain/cross_studies_metadata/cross_studies_metadata.html.

### Author(s)

Leonardo Collado-Torres

### References

Razmara et al, in prep, 2018.

### Examples

    ## Add the sample metadata to an example rse_gene object
    rse_gene <- add_metadata(rse_gene_SRP009615, 'recount_brain_v1')

    ## Explore the metadata
    colData(rse_gene)

    ## For a list of studies present in recount_brain_v1 check
    ## http://lieberinstitute.github.io/recount-brain/. Note that it only
    ## includes studies from SRA, so no TCGA or GTEx (those have great
    ## sample metadata already available).
    ## recount_brain_v2 includes GTEx and TCGA brain samples in addition to the
    ## recount_brain_v1 data.

    ## Not run:
    ## Example project that is present in recount_brain_v2.

    ## Download and load the data
    download_study('ERP001304')
    load(file.path('ERP001304', 'rse_gene.Rdata'))

    ## Add the sample metadata from recount_brain_v2
    rse_gene <- add_metadata(rse_gene, source = 'recount_brain_v2')

    ## Check the metadata
    colData(rse_gene)

    ## End(Not run)

    ## Obtain all the recount_brain_v2 metadata
    recount_brain_v2 <- add_metadata(source = 'recount_brain_v2')

[Package recount version 1.8.2 Index]