available_samples {recount3} | R Documentation |
This function returns a data.frame()
with the samples that are available
from recount3
. Note that a specific sample might be available from a
given data_source
and none or many collections
.
available_samples( organism = c("human", "mouse"), recount3_url = getOption("recount3_url", "http://duffel.rail.bio/recount3"), bfc = recount3_cache(), verbose = getOption("recount3_verbose", TRUE), available_homes = project_homes(organism = organism, recount3_url = recount3_url) )
organism |
A |
recount3_url |
A |
bfc |
A BiocFileCache-class
object where the files will be cached to, typically created by
|
verbose |
A |
available_homes |
A |
A data.frame()
with the sample ID used by the original source of
the data (external_id
), the project ID (project
), the organism
, the
file_source
from where the data was accessed, the date the sample
was processed (date_processed
) in YYYY-MM-DD
format,
the recount3
project home location (project_home
), and the project
project_type
that differentiates between data_sources
and compilations
.
## Find all the human samples available from recount3 human_samples <- available_samples() dim(human_samples) head(human_samples) ## How many are from a data source vs a compilation? table(human_samples$project_type, useNA = "ifany") ## What are the unique file sources? table( human_samples$file_source[human_samples$project_type == "data_sources"] ) ## Find all the mouse samples available from recount3 mouse_samples <- available_samples("mouse") dim(mouse_samples) head(mouse_samples) ## How many are from a data source vs a compilation? table(mouse_samples$project_type, useNA = "ifany")