Generate tables used for generate_prioritization_tables

Calculate differential expression, average expression, and condition specificity of ligands and receptors.

Usage

generate_info_tables(
  seuratObj,
  celltype_colname,
  senders_oi,
  receivers_oi,
  lr_network_filtered,
  condition_colname = NULL,
  condition_oi = NULL,
  condition_reference = NULL,
  scenario = "case_control",
  assay_oi = NULL,
  ...
)

Arguments

seuratObj

Seurat object

celltype_colname

Name of the meta data column that indicates the cell type of a cell

senders_oi

Default NULL: all celltypes will be considered as senders. If you want to select specific senders of interest: you can add this here as character vector.

receivers_oi

Default NULL: all celltypes will be considered as receivers If you want to select specific receivers of interest: you can add this here as character vector.

lr_network_filtered

Ligand-receptor network that has been filtered to only contain ligands and receptors that are expressed

condition_colname

Name of the meta data column that indicates from which group/condition a cell comes from

condition_oi

If provided, subset seurat_obj so DE is only calculated for cells belonging to condition_oi

condition_reference

Reference condition for condition specificity calculation

scenario

"case_control" or "one_condition": if "case_control", calculate condition specificity. If "one_condition", only calculate cell type specificity.

assay_oi

Which assay need to be used for DE calculation. If NULL, will use DefaultAssay

...

Arguments passed to FindAllMarkers, FindMarkers, and AverageExpression

Value

List of dataframes containing sender-receiver DE, sender-receiver expression, and condition DE