add_metadata: Add additional curated metadata to a recount rse object

In leekgroup/recount: Explore and download data from the recount project

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")

leekgroup/recount documentation built on May 24, 2024, 11:19 a.m.