scfetch (version 0.5.0)

ParseHCA: Download Human Cell Atlas Datasets.

Description

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
)

Value

Dataframe contains failed projects or NULL.

Arguments

meta

Metadata used to download, can be from ExtractHCAMeta, should contain entryId and name catalog.

file.ext

The valid file extension for download. When NULL, use "rds", "rdata", "h5", "h5ad", "loom". Default: c("rds", "rdata", "h5", "h5ad", "loom").

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).

Examples

if (FALSE) {
# 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, need users to provide the output folder
ParseHCA(meta = all.human.10x.projects, out.folder = "/path/to/output")
}