files {hca} | R Documentation |
files()
takes a list of user provided project titles
to be used to query the HCA API for information about available files.
files_download()
takes a tibble of files and a directory
location as arguments to download the files of the tibble into the specified
directory.
files_detail()
takes a unique file_id and catalog for
the file, and returns details about the specified file as a
list-of-lists
files_cache()
is the default location of the cache
of downloaded files.
files( filters = NULL, size = 1000L, sort = "projectTitle", order = c("asc", "desc"), catalog = NULL, as = c("tibble", "lol", "list"), columns = files_default_columns("character") ) files_default_columns(as = c("tibble", "character")) files_download(tbl, destination = NULL) files_facets(facet = character(), catalog = NULL) files_detail(uuid, catalog = NULL) files_cache(create = FALSE)
filters |
filter object created by |
size |
integer(1) maximum number of results to return;
default: all projects matching |
sort |
character(1) project facet (see |
order |
character(1) sort order. One of |
catalog |
character(1) source of data. Use
|
as |
character(1) return format. Default: |
columns |
named character() indicating the paths to be used
for parsing the 'lol' returned from the HCA to a tibble. The
names of |
tbl |
tibble of files (result of |
destination |
character() vector name of temporary directory to use
for file downloads, or |
facet |
character() of valid facet names. Summary results (see 'Value', below) are returned when missing or length greater than 1; details are returned when a single facet is specified. |
uuid |
character() unique identifier (e.g., |
create |
logical(1) create the default cache location, if it does not yet exist. |
files_cache()
can be useful when it is necessary to
'clean up' the cache, e.g., BiocFileCache::cleanbfc()
or more
dramatically unlink(files_cache(), recursive = TRUE)
.
files_download()
returns a character() vector of file
destinations
files_detail()
returns a list-of-lists containing
relevant details about the file.
files_cache()
returns the path to the default cache. Use
this as the cache=
argument to BiocFileCache()
.
title <- paste( "Tabula Muris: Transcriptomic characterization of 20 organs and tissues from Mus musculus", "at single cell resolution" ) filters <- filters( projectTitle = list(is = title) ) files(filters = filters) files_filter <- filters( projectId = list(is = "cddab57b-6868-4be4-806f-395ed9dd635a"), fileFormat = list(is = "loom") ) files_tbl <- files(filter = files_filter, catalog = "dcp1") ## Not run: files_download(files_tbl, destination = tempdir()) files_facets() files_facets("fileFormat") files_detail( uuid = "ee6a75bd-3252-41ee-b253-425bbd377f0c", catalog = "dcp1" ) files_cache(create = FALSE)