Filter ligand-receptor database by expression — filter_lr

Filter LR pairs to keep only those with sufficient expression in the dataset.

Usage

filter_lr_database(
  df_ligrec,
  seurat_obj,
  assay = NULL,
  slot = "data",
  heteromeric = TRUE,
  heteromeric_delimiter = "_",
  heteromeric_rule = c("min", "ave"),
  min_cell = 100L,
  min_cell_pct = 0.05,
  verbose = TRUE
)

Arguments

df_ligrec: Data frame from ligand_receptor_database.
seurat_obj: Seurat object with expression data.
assay: Assay to use (default: DefaultAssay).
slot: Expression slot/layer (default: "data").
heteromeric: Whether ligands/receptors can be multi-subunit complexes (default: TRUE).
heteromeric_delimiter: Character separating subunit genes (default: "_").
heteromeric_rule: Aggregation rule for complex expression: "min" (default) uses minimum subunit, "ave" uses average.
min_cell: Minimum number of cells expressing (alternative criterion).
min_cell_pct: Minimum percentage of cells expressing (default: 0.05).
verbose: Print progress messages (default: TRUE).

Value

Filtered data frame of ligand-receptor pairs.

Examples

if (FALSE) { # \dontrun{
df_lr <- ligand_receptor_database("CellChat", "mouse")
df_lr_filtered <- filter_lr_database(df_lr, seurat_obj, min_cell_pct = 0.05)
} # }