add_metadata {recount} | R Documentation |
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/.
add_metadata(rse, source = "recount_brain_v1", is_tcga = FALSE, verbose = TRUE)
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 |
is_tcga |
Set to |
verbose |
If |
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')[5].
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.
Leonardo Collado-Torres
Razmara et al, bioRxiv, 2019. https://www.biorxiv.org/content/10.1101/618025v1
## 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')