scfetch (version 0.5.0)

ParsePanglaoDB: Parse PanglaoDB Data.

Description

Parse PanglaoDB Data.

Usage

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

Value

Seurat object (if merge is TRUE) or list of Seurat objects (if merge is FALSE).

Arguments

meta

Metadata contains "SRA", "SRS", "Tissue", "Protocol", "Species", can be obtained with ExtractPanglaoDBMeta.

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.

Examples

if (FALSE) {
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)
}