ParsePanglaoDB: Parse PanglaoDB Data.

In scfetch: Access and Format Single-Cell RNA-Seq Datasets from Public Resources

Parse PanglaoDB Data.

Description

Parse PanglaoDB Data.

Usage

ParsePanglaoDB(
  meta,
  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.
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

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

Examples

## Not run: 
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)

## End(Not run)

scfetch documentation built on Nov. 22, 2023, 1:09 a.m.