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()
#> 2024-12-10 22:01:29.182618 caching file sra.recount_project.MD.gz.
#> 2024-12-10 22:01:29.614085 caching file gtex.recount_project.MD.gz.
#> 2024-12-10 22:01:30.035782 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)
#> 2024-12-10 22:01:31.842301 downloading and reading the metadata.
#> 2024-12-10 22:01:32.25808 caching file sra.sra.SRP009615.MD.gz.
#> 2024-12-10 22:01:32.722892 caching file sra.recount_project.SRP009615.MD.gz.
#> 2024-12-10 22:01:33.154502 caching file sra.recount_qc.SRP009615.MD.gz.
#> 2024-12-10 22:01:33.700977 caching file sra.recount_seq_qc.SRP009615.MD.gz.
#> 2024-12-10 22:01:34.149767 caching file sra.recount_pred.SRP009615.MD.gz.
#> 2024-12-10 22:01:34.208994 downloading and reading the feature information.
#> 2024-12-10 22:01:34.642825 caching file human.gene_sums.G026.gtf.gz.
#> 2024-12-10 22:01:35.003811 downloading and reading the counts: 12 samples across 63856 features.
#> 2024-12-10 22:01:35.375571 caching file sra.gene_sums.SRP009615.G026.gz.
#> 2024-12-10 22:01:35.509445 constructing the RangedSummarizedExperiment (rse) object.
## Expand the SRA attributes (see details for more information)
rse_gene_SRP009615 <- expand_sra_attributes(rse_gene_SRP009615)