LoadCellPhoneDB: Load CellPhoneDB Datasets

In stevexniu/scMatchmaker: Single Cell Matchmaker

Load CellPhoneDB Datasets

Description

Load the CellPhoneDB dataset for ligand-receptor interaction pairs.

Usage

LoadCellPhoneDB(
  interaction_input,
  gene_input,
  complex_input,
  gene.symbol = "gene_name",
  annotation.strategy = NULL,
  invert = FALSE,
  path = FALSE,
  url = FALSE
)

Arguments

interaction_input	Data frame (csv file), directory path or URL of the interaction_input file.
gene_input	Data frame (csv file), directory path or URL of the gene_input file.
complex_input	Data frame (csv file), directory path or URL of the complex_input file.
gene.symbol	Gene symbols to use. The possible names are listed as column names in the gene_input file. Examples include: gene_name, uniprot, hgnc_symbol, ensembl. Default is gene_name.
annotation.strategy	Annotation strategy used. Default is NULL, possible options include "curated" etc.
invert	Whether to perfrom invert selection on annotation strategy. Default is FALSE
path	Whether inputs are in directory path format.
url	Whether inputs are in URl format.

Value

Returns the interaction pairs data.frame with the first two columns correspond to interacting partners.

Examples

## Not run: 
# CellPhoneDB URLs 
pair.data <- LoadCellPhoneDB(
 interaction_input = interaction_input.url,
 gene_input = gene_input.url,
 complex_input = complex_input.url,
 gene.symbol = "ensembl", annotation.strategy = "curated", url = TRUE)

## End(Not run)

stevexniu/scMatchmaker documentation built on June 2, 2022, 12:35 p.m.