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().
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()
#> 2023-05-07 00:12:18.971639 caching file sra.recount_project.MD.gz.
#> 2023-05-07 00:12:19.291246 caching file gtex.recount_project.MD.gz.
#> 2023-05-07 00:12:19.631356 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)
#> 2023-05-07 00:12:21.845299 downloading and reading the metadata.
#> 2023-05-07 00:12:22.180084 caching file sra.sra.SRP009615.MD.gz.
#> 2023-05-07 00:12:22.496025 caching file sra.recount_project.SRP009615.MD.gz.
#> 2023-05-07 00:12:22.814289 caching file sra.recount_qc.SRP009615.MD.gz.
#> 2023-05-07 00:12:23.151212 caching file sra.recount_seq_qc.SRP009615.MD.gz.
#> 2023-05-07 00:12:23.475999 caching file sra.recount_pred.SRP009615.MD.gz.
#> 2023-05-07 00:12:23.558369 downloading and reading the feature information.
#> 2023-05-07 00:12:23.841686 caching file human.gene_sums.G026.gtf.gz.
#> 2023-05-07 00:12:24.337531 downloading and reading the counts: 12 samples across 63856 features.
#> 2023-05-07 00:12:24.608303 caching file sra.gene_sums.SRP009615.G026.gz.
#> 2023-05-07 00:12:24.787148 constructing the RangedSummarizedExperiment (rse) object.
## Expand the SRA attributes (see details for more information)
rse_gene_SRP009615 <- expand_sra_attributes(rse_gene_SRP009615)