rliger (version 2.0.1)

importPBMC: Import prepared dataset publically available

Description

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),
  ...
)

Value

Constructed liger object with QC performed and missing data removed.

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

Examples

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