scfetch (version 0.5.0)

ExtractPanglaoDBComposition: Extract Cell Type Composition of PanglaoDB Datasets.

Description

Extract Cell Type Composition of PanglaoDB Datasets.

Usage

ExtractPanglaoDBComposition(
  sra = NULL,
  srs = NULL,
  species = NULL,
  protocol = NULL,
  tissue = NULL,
  local.data = TRUE
)

Value

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

Arguments

sra

The SRA identifier of the datasets, obtain available values with StatDBAttribute, one or multiple value. Default: NULL (All).

srs

The SRS identifier of the datasets, obtain available values with StatDBAttribute, one or multiple value. Default: NULL (All).

species

The species of the datasets, choose from "Homo sapiens", "Mus musculus", one or multiple value. Default: NULL (All).

protocol

Protocol used to generate the datasets, choose from "10x chromium", "drop-seq", "microwell-seq", "C1 Fluidigm", "inDrops", "Smart-seq2", "CEL-seq", one or multiple value. Default: NULL (All).

tissue

The tissue of the datasets, obtain available values with StatDBAttribute, one or multiple value. Default: NULL (All).

local.data

Logical value, whether to use local data (PanglaoDB is no longer maintained).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

Examples

# \donttest{
human.composition <- ExtractPanglaoDBComposition(
  species = "Homo sapiens",
  protocol = c("Smart-seq2", "10x chromium")
)
# }