Extract Cell Type Composition of PanglaoDB Datasets.

Extract Cell Type Composition of PanglaoDB Datasets.

Usage

ExtractPanglaoDBComposition(
  meta = NULL,
  sra = NULL,
  srs = NULL,
  local.data = TRUE
)

Arguments

meta

Metadata contains "SRA", "SRS", 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.

local.data

Logical value, whether to use local data (PanglaoDB is no longer maintained). Default: TRUE.

Value

Dataframe contains sample metadata, cluster, cell number and cell type information.

Examples

# \donttest{
# get metadata
human.meta <- ExtractPanglaoDBMeta(
  species = "Homo sapiens",
  protocol = c("Smart-seq2", "10x chromium"),
  cell.num = c(1000, 2000)
)
# get composition
human.composition <- ExtractPanglaoDBComposition(
  meta = human.meta
)
# given dataset
human.composition <- ExtractPanglaoDBComposition(sra = "SRA598936")
# human.composition <- ExtractPanglaoDBComposition(srs = "SRS2428405")
# human.composition <- ExtractPanglaoDBComposition(sra = "SRA598936", srs = "SRS2428405")
# }