Processing differential expression output of the receiver cell types

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

if (FALSE) { # \dontrun{
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)
} # }