Parse PanglaoDB Data.

Usage

ParsePanglaoDB(
  meta = NULL,
  sra = NULL,
  srs = NULL,
  cell.type = "All",
  include.gene = NA,
  exclude.gene = NA,
  merge = FALSE
)

Arguments

meta: Metadata contains "SRA", "SRS", "Tissue", "Protocol", "Species", can be obtained with ExtractPanglaoDBMeta. Skip when sra or srs is not NULL. Default: NULL.
sra: The SRA identifier of the datasets. Skip when meta or srs is not NULL. Default: NULL.
srs: The SRS identifier of the datasets. Skip when meta or sra is not NULL. Default: NULL.
cell.type: Extract samples with specified cell types. For samples without SRS (notused), this value can only be "All" or "None", or these samples will be filtered. Obtain available values with StatDBAttribute, one or multiple value. Default: "All".
include.gene: Include cells expressing the genes. Default: NA.
exclude.gene: Exclude cells expressing the genes. Default: NA.
merge: Logical value, whether to merge Seurat list. Default: FALSE.

Value

SeuratObject (if merge is TRUE) or list of SeuratObjects (if merge is FALSE).

Examples

if (FALSE) { # \dontrun{
hsa.meta <- ExtractPanglaoDBMeta(
  species = "Homo sapiens",
  protocol = c("Smart-seq2", "10x chromium"),
  show.cell.type = TRUE, cell.num = c(1000, 2000)
)
hsa.seu <- ParsePanglaoDB(hsa.meta, merge = TRUE)
# load given dataset
cortex.seu <- ParsePanglaoDB(sra = "SRA598936", srs = "SRS2428405")
# cortex.seu = ParsePanglaoDB(srs = "SRS2428405")
# cortex.seu = ParsePanglaoDB(sra = "SRA598936")
} # }