combine_sender_receiver_de: Combine the differential expression information of ligands in...

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

Combine the differential expression information of ligands in the sender celltypes with the differential expression information of their cognate receptors in the receiver cell types

Description

combine_sender_receiver_de Combine the differential expression information of ligands in the sender celltypes with the differential expression information of their cognate receptors in the receiver cell types.

Usage

combine_sender_receiver_de(DE_sender_processed, DE_receiver_processed, lr_network, specificity_score = "min_lfc")

Arguments

DE_sender_processed	Output of 'process_niche_de' with 'type = receiver'
DE_receiver_processed	Output of 'process_niche_de' with 'type = receiver'
lr_network	Ligand-Receptor Network in tibble format: ligand, receptor as columns
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 giving the differential expression information of ligands in the sender celltypes and their cognate receptors in the receiver cell types.

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_sender = calculate_niche_de(seurat_obj, niches, "sender")
DE_receiver = calculate_niche_de(seurat_obj, niches, "receiver")
expression_pct = 0.10
DE_sender_processed = process_niche_de(DE_table = DE_sender, niches = niches, expression_pct = expression_pct, type = "sender")
DE_receiver_processed = process_niche_de(DE_table = DE_receiver, niches = niches, expression_pct = expression_pct, type = "receiver")
specificity_score_LR_pairs = "min_lfc"
DE_sender_receiver = combine_sender_receiver_de(DE_sender_processed, DE_receiver_processed, lr_network, specificity_score = specificity_score_LR_pairs)

## End(Not run)

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