Download Human Cell Atlas Datasets.

Usage

ParseHCA(
  meta = NULL,
  link = NULL,
  file.ext = c("rds", "rdata", "h5", "h5ad", "loom", "tsv"),
  out.folder = NULL,
  timeout = 3600,
  quiet = FALSE,
  parallel = TRUE,
  use.cores = NULL,
  return.seu = FALSE,
  merge = TRUE
)

Arguments

meta: Metadata used to download, can be from ExtractHCAMeta. Skip when link is not NULL. Default: NULL.
link: Vector contains project link(s), e.g. "https://explore.data.humancellatlas.org/projects/902dc043-7091-445c-9442-d72e163b9879". Skip when meta is not NULL. Default: NULL.
file.ext: The valid file extension for download. When NULL, use "rds", "rdata", "h5", "h5ad", "loom", "tsv". Default: c("rds", "rdata", "h5", "h5ad", "loom", "tsv").
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).
use.cores: The number of cores used. Default: NULL (the minimum value of extracted length(download.urls) and parallel::detectCores()).
return.seu: Logical value, whether to load downloaded datasets to Seurat. Valid when rds in file.ext and all datasets download successfully. Default: FALSE.
merge: Logical value, whether to merge Seurat list when there are multiple rds files, used when return.seu is TRUE. Default: FALSE.

Value

SeuratObject (return.seu is TRUE, rds in file.ext) or list contains files' metadata of downloaded successfully (down.meta) and failed (fail.meta).

Examples

if (FALSE) { # \dontrun{
# 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")
# download given projects
ParseHCA(
  link = c(
    "https://explore.data.humancellatlas.org/projects/902dc043-7091-445c-9442-d72e163b9879",
    "https://explore.data.humancellatlas.org/projects/cdabcf0b-7602-4abf-9afb-3b410e545703"
  ),
  out.folder = "/path/to/output"
)
} # }