process_receiver_target_de: Processing differential expression output of the receiver...

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

Processing differential expression output of the receiver cell types

Description

process_receiver_target_de Processing differential expression output of the receiver cell types – used before ligand-activity and ligand-target inference.

Usage

process_receiver_target_de(DE_receiver_targets, niches, expression_pct, specificity_score = "min_lfc")

Arguments

DE_receiver_targets	Output of 'calculate_niche_de' with 'type = receiver'
niches	a list of lists/niches giving the name, senders and receiver celltypes for each nice. Sender and receiver cell types should be part of Idents(seurat_obj).
expression_pct	Percentage of cells of a cell type having a non-zero expression value for a gene such that a gene can be considered expressed by that cell type.
specificity_score	Defines which score will be used to prioritze ligand-receptor pairs and consider their differential expression. Default and recommended: "min_lfc". "min_lfc" looks at the minimal logFC of the ligand/receptor between the celltype of interest and all the other celltypes. Alternatives: "mean_lfc", "min_score", and "mean_score". Mean uses the average/mean instead of minimum. score is the product of the logFC and the ratio of fraction of expressing cells.

Value

A tibble containing the processed DE information of the receiver cell types – used before ligand-activity and ligand-target inference.

Examples

## Not run: 
seurat_obj = readRDS(url("https://zenodo.org/record/5840787/files/seurat_obj_subset_integrated_zonation.rds"))
niches = list(
"KC_niche" = list(
  "sender" = c("LSECs_portal","Hepatocytes_portal","Stellate cells_portal"),
  "receiver" = c("KCs")),
"MoMac2_niche" = list(
  "sender" = c("Cholangiocytes","Fibroblast 2"),
  "receiver" = c("MoMac2")),
"MoMac1_niche" = list(
  "sender" = c("Capsule fibroblasts","Mesothelial cells"),
 "receiver" = c("MoMac1"))
)
DE_receiver = calculate_niche_de(seurat_obj, niches, "receiver")
expression_pct = 0.10
DE_receiver_processed = process_receiver_target_de(DE_receiver_targets = DE_receiver, niches = niches, expression_pct = expression_pct)

## End(Not run)

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