Download Human Cell Atlas Datasets.

Usage

ParseHCA(
  meta,
  file.ext = c("rds", "rdata", "h5", "h5ad", "loom"),
  out.folder = NULL,
  timeout = 3600,
  quiet = FALSE,
  parallel = TRUE
)

Arguments

meta: Metadata used to download, can be from ExtractHCAMeta, should contain entryId and name catalog.
out.folder: The output folder. Default: NULL (current working directory).
timeout: Maximum request time. Default: 3600.
quiet: Logical value, whether to show downloading progress. Default: FALSE (show).
parallel: Logical value, whether to download parallelly. Default: TRUE. When "libcurl" is available for download.file, the parallel is done by default (parallel can be FALSE).
file.ext.: The valid file extension for download. When NULL, use "rds", "rdata", "h5", "h5ad", "loom". Default: c("rds", "rdata", "h5", "h5ad", "loom").

Value

Dataframe contains failed projects or NULL.

Examples

# # all available projects
# all.hca.projects = ShowHCAProjects()
# # all human and 10x 3' v2
# all.human.10x.projects = ExtractHCAMeta(all.projects.df = all.hca.projects,  organism = "Homo sapiens",
#                                         protocol = c("10x 3' v2", "10x 3' v3"))
# # download
# ParseHCA(meta = all.human.10x.projects, out.folder = "/path/to/output")