locate_url {recount3} | R Documentation |
recount3
fileGiven an organism of interest, this function constructs the URL for accessing
one of the output files from the recount3
project. You can then download
the file using file_retrieve()
.
locate_url( project, project_home = project_homes(organism = organism, recount3_url = recount3_url), type = c("metadata", "gene", "exon", "jxn", "bw"), organism = c("human", "mouse"), sample = NULL, annotation = annotation_options(organism), jxn_format = c("ALL", "UNIQUE"), recount3_url = getOption("recount3_url", "http://duffel.rail.bio/recount3") )
project |
A |
project_home |
A |
type |
A |
organism |
A |
sample |
A |
annotation |
A |
jxn_format |
A |
recount3_url |
A |
A character()
with the URL(s) for the file(s) of interest.
Other internal functions for accessing the recount3 data:
annotation_ext()
,
create_rse_manual()
,
file_retrieve()
,
locate_url_ann()
,
project_homes()
,
read_counts()
,
read_metadata()
## Example for metadata files from a project from SRA locate_url( "SRP009615", "data_sources/sra" ) ## Example for metadata files from a project that is part of a collection locate_url( "ERP110066", "collections/geuvadis_smartseq", recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3" ) ## Example for a BigWig file locate_url( "SRP009615", "data_sources/sra", "bw", "human", "SRR387777" ) ## Locate example gene count files locate_url( "SRP009615", "data_sources/sra", "gene" ) locate_url( "SRP009615", "data_sources/sra", "gene", annotation = "refseq" ) ## Example for a gene count file from a project that is part of a collection locate_url( "ERP110066", "collections/geuvadis_smartseq", "gene", recount3_url = "http://snaptron.cs.jhu.edu/data/temp/recount3" ) ## Locate example junction files locate_url( "SRP009615", "data_sources/sra", "jxn" ) ## Example for metadata files from a project from SRA locate_url( "ERP001942", "data_sources/sra" )