generate_info_tables: Generate tables used for 'generate_prioritization_tables'

In saeyslab/nichenetr: NicheNet: Modeling Intercellular Communication by Linking Ligands to Target Genes

Generate tables used for generate_prioritization_tables

Description

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

saeyslab/nichenetr documentation built on April 27, 2024, 9:24 p.m.