Description Usage Arguments Details Value Author(s) References Examples
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/.
1 | add_metadata(rse, source = "recount_brain_v2", 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 |
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').
A RangedSummarizedExperiment-class
object with the sample metadata columns appended to the colData()
slot.
Leonardo Collado-Torres
Razmara et al, bioRxiv, 2019. https://www.biorxiv.org/content/10.1101/618025v1
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ## 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")
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.