Load CellPhoneDB Datasets — LoadCellPhoneDB • scMatchmaker

Load the CellPhoneDB dataset for ligand-receptor interaction pairs.

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

if (FALSE) {
# 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)
}