This function expands the SRA attributes stored in sra.sample_attributes
variable in the colData() slot of a
RangedSummarizedExperiment-class
produced by create_rse().
expand_sra_attributes(rse)A RangedSummarizedExperiment-class
object created by create_rse() or create_rse_manual().
A RangedSummarizedExperiment-class object with expanded metadata columns.
Note that this function will work on projects available from SRA only.
Furthermore, SRA attributes are project-specific. Thus, if you use this
function in more than one RSE object, you won't be able to combine them
easily with cbind() and will need to manually merge the colData() slots
from your set of RSE files before being able to run cbind().
## Find all available human projects
human_projects <- available_projects()
#> 2025-09-24 22:48:45.948417 caching file sra.recount_project.MD.gz.
#> 2025-09-24 22:48:46.738868 caching file gtex.recount_project.MD.gz.
#> 2025-09-24 22:48:47.311536 caching file tcga.recount_project.MD.gz.
## Find the project you are interested in
proj_info <- subset(
human_projects,
project == "SRP009615" & project_type == "data_sources"
)
## Create a RSE object at the gene level
rse_gene_SRP009615 <- create_rse(proj_info)
#> 2025-09-24 22:48:49.880167 downloading and reading the metadata.
#> 2025-09-24 22:48:50.704225 caching file sra.sra.SRP009615.MD.gz.
#> 2025-09-24 22:48:51.685219 caching file sra.recount_project.SRP009615.MD.gz.
#> 2025-09-24 22:48:52.606729 caching file sra.recount_qc.SRP009615.MD.gz.
#> 2025-09-24 22:48:53.133553 caching file sra.recount_seq_qc.SRP009615.MD.gz.
#> 2025-09-24 22:48:53.935569 caching file sra.recount_pred.SRP009615.MD.gz.
#> 2025-09-24 22:48:54.00144 downloading and reading the feature information.
#> 2025-09-24 22:48:54.934797 caching file human.gene_sums.G026.gtf.gz.
#> 2025-09-24 22:48:55.296659 downloading and reading the counts: 12 samples across 63856 features.
#> 2025-09-24 22:48:55.885535 caching file sra.gene_sums.SRP009615.G026.gz.
#> 2025-09-24 22:48:56.020876 constructing the RangedSummarizedExperiment (rse) object.
## Expand the SRA attributes (see details for more information)
rse_gene_SRP009615 <- expand_sra_attributes(rse_gene_SRP009615)