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Filter ligand-receptor pairs by expression threshold

Source: R/filterLRpairs.R
filterLRpairs.Rd

Retains only LR pairs where at least one bin/spot has counts at or above min_ligand for every ligand subunit and min_receptor for every receptor subunit.

Usage

filterLRpairs(
  counts,
  min_ligand = 10,
  min_receptor = 10,
  LR_df = NULL,
  species = c("human", "mouse")
)

Arguments

counts

Gene-by-bin count matrix (dense or sparse). Row names must be gene symbols.

min_ligand

Numeric. Minimum count threshold for ligand genes. At least one bin must meet or exceed this value. Default 10.

min_receptor

Numeric. Minimum count threshold for receptor genes. At least one bin must meet or exceed this value. Default 10.

LR_df

Data frame of ligand-receptor pairs with columns ligand.symbol and receptor.symbol (comma-separated gene symbols for multi-subunit complexes). When NULL, the CellChatDB for the chosen species is downloaded automatically.

species

Character. Which CellChatDB to download when LR_df is NULL. One of "human" (default) or "mouse".

Value

A subset of LR_df containing only pairs that pass the expression thresholds for both ligand and receptor.

Examples

if (FALSE) { # \dontrun{
# Supply a small custom LR_df to avoid a network download
LR_df <- data.frame(
  ligand.symbol   = c("GENE1", "GENE3"),
  receptor.symbol = c("GENE2", "GENE4"),
  annotation      = c("Secreted Signaling", "ECM-Receptor"),
  row.names       = c("LR1", "LR2")
)
set.seed(1)
counts <- matrix(
  rpois(4 * 50, lambda = c(20, 1, 5, 20)), nrow = 4, ncol = 50,
  dimnames = list(c("GENE1", "GENE2", "GENE3", "GENE4"),
                  paste0("bin_", 1:50))
)
filterLRpairs(counts, min_ligand = 10, min_receptor = 10, LR_df = LR_df)
} # }