expand_sra_attributes {recount3} | R Documentation |
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)
rse |
A RangedSummarizedExperiment-class
object created by |
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()
.
A RangedSummarizedExperiment-class object with expanded metadata columns.
Andrew E Jaffe modified by Leonardo Collado-Torres.
## Find all available human projects human_projects <- available_projects() ## 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) ## Expand the SRA attributes (see details for more information) rse_gene_SRP009615 <- expand_sra_attributes(rse_gene_SRP009615)