Import prepared dataset publically available

These are functions to download example datasets that are subset from public data.

PBMC - Downsampled from GSE96583, Kang et al, Nature Biotechnology, 2018. Contains two scRNAseq datasets.
BMMC - Downsampled from GSE139369, Granja et al, Nature Biotechnology, 2019. Contains two scRNAseq datasets and one scATAC data.
CGE - Downsampled from GSE97179, Luo et al, Science, 2017. Contains one scRNAseq dataset and one DNA methylation data.

Usage

importPBMC(
  dir = getwd(),
  overwrite = FALSE,
  method = "libcurl",
  verbose = getOption("ligerVerbose", TRUE),
  ...
)

importBMMC(
  dir = getwd(),
  overwrite = FALSE,
  method = "libcurl",
  verbose = getOption("ligerVerbose", TRUE),
  ...
)

importCGE(
  dir = getwd(),
  overwrite = FALSE,
  method = "libcurl",
  verbose = getOption("ligerVerbose", TRUE),
  ...
)

Arguments

dir: Path to download datasets. Default current working directory getwd().
overwrite: Logical, if a file exists at corresponding download location, whether to re-download or directly use this file. Default FALSE.
method: method argument directly passed to download.file. Using "libcurl" while other options might not work depending on platform.
verbose: Logical. Whether to show information of the progress. Default getOption("ligerVerbose") or TRUE if users have not set.
...: Additional arguments passed to download.file

Value

Constructed liger object with QC performed and missing data removed.

Examples

if (FALSE) { # interactive()
# \donttest{
pbmc <- importPBMC()
bmmc <- importBMMC()
cge <- importCGE()
# }
}