calculate_niche_de_targets: Calculate differential expression of receiver cell type in...

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

Calculate differential expression of receiver cell type in one niche versus all other niches of interest: focus on finding DE genes

Description

calculate_niche_de_targets Calculate differential expression of receiver cell type in one niche versus all other niches of interest: focus on finding DE genes

Usage

calculate_niche_de_targets(seurat_obj, niches, expression_pct, lfc_cutoff, assay_oi = "SCT")

Arguments

seurat_obj	Seurat object
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	input of 'min.pct' of 'Seurat::FindMarkers'
lfc_cutoff	input of 'logfc.threshold' of 'Seurat::FindMarkers'
assay_oi	Which assay need to be used for DE calculation via 'FindMarkers'. Default SCT, alternatives: RNA.

Value

A tibble containing the DE results of the niches versus each other.

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"))
)
calculate_niche_de_targets(seurat_obj, niches, expression_pct = 0.10, lfc_cutoff = 0.15)

## End(Not run)

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