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()
#> 2026-04-01 03:50:11.039402 caching file sra.recount_project.MD.gz.
#> 2026-04-01 03:50:11.353852 caching file gtex.recount_project.MD.gz.
#> 2026-04-01 03:50:11.647563 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)
#> 2026-04-01 03:50:13.414474 downloading and reading the metadata.
#> 2026-04-01 03:50:13.687777 caching file sra.sra.SRP009615.MD.gz.
#> 2026-04-01 03:50:13.93008 caching file sra.recount_project.SRP009615.MD.gz.
#> 2026-04-01 03:50:14.222841 caching file sra.recount_qc.SRP009615.MD.gz.
#> 2026-04-01 03:50:14.507212 caching file sra.recount_seq_qc.SRP009615.MD.gz.
#> 2026-04-01 03:50:14.759171 caching file sra.recount_pred.SRP009615.MD.gz.
#> 2026-04-01 03:50:14.824837 downloading and reading the feature information.
#> 2026-04-01 03:50:15.164634 caching file human.gene_sums.G026.gtf.gz.
#> 2026-04-01 03:50:15.645442 downloading and reading the counts: 12 samples across 63856 features.
#> 2026-04-01 03:50:15.984828 caching file sra.gene_sums.SRP009615.G026.gz.
#> 2026-04-01 03:50:16.116612 constructing the RangedSummarizedExperiment (rse) object.
## Expand the SRA attributes (see details for more information)
rse_gene_SRP009615 <- expand_sra_attributes(rse_gene_SRP009615)