available_projects {recount3} | R Documentation |
List available projects in recount3
available_projects( organism = c("human", "mouse"), recount3_url = getOption("recount3_url", "http://duffel.rail.bio/recount3"), bfc = recount3_cache(), 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
|
available_homes |
A |
A data.frame()
with the project ID (project
), the organism
, the
file_source
from where the data was accessed,
the recount3
project home location (project_home
), the project
project_type
that differentiates between data_sources
and compilations
,
the n_samples
with the number of samples in the given project.
## Find all the human projects human_projects <- available_projects() ## Explore the results dim(human_projects) head(human_projects) ## How many are from a data source vs a compilation? table(human_projects$project_type, useNA = "ifany") ## What are the unique file sources? table( human_projects$file_source[human_projects$project_type == "data_sources"] ) ## Note that big projects are broken up to make them easier to access ## For example, GTEx and TCGA are broken up by tissue head(subset(human_projects, file_source == "gtex")) head(subset(human_projects, file_source == "tcga")) ## Find all the mouse projects mouse_projects <- available_projects(organism = "mouse") ## Explore the results dim(mouse_projects) head(mouse_projects) ## How many are from a data source vs a compilation? table(mouse_projects$project_type, useNA = "ifany") ## What are the unique file sources? table( mouse_projects$file_source[mouse_projects$project_type == "data_sources"] ) ## Use with a custom recount3_url: available_projects( recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3test", available_homes = "data_sources/sra" ) ## You can also rely on project_homes() if the custom URL has a text file ## that can be read with readLines() at: ## <recount3_url>/<organism>/homes_index available_projects( recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3test" )