combine_sender_receiver_de: combine_sender_receiver_de

In saeyslab/multinichenetr: MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

combine_sender_receiver_de

Description

combine_sender_receiver_de Combine Muscat differential expression output for senders and receivers by linkgin ligands to receptors based on the prior knowledge ligand-receptor network.

Usage

combine_sender_receiver_de(sender_de, receiver_de, senders_oi, receivers_oi, lr_network)

Arguments

sender_de	Differential expression analysis output for the sender cell types. 'de_output_tidy' slot of the output of 'perform_muscat_de_analysis'.
receiver_de	Differential expression analysis output for the receiver cell types. 'de_output_tidy' slot of the output of 'perform_muscat_de_analysis'.
senders_oi	Default NULL: all celltypes will be considered as senders. If you want to select specific senders_oi: 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_oi: you can add this here as character vector.
lr_network	Prior knowledge Ligand-Receptor network (columns: ligand, receptor)

Value

Data frame combining Muscat DE output for sender and receiver linked to each other through joining by the ligand-receptor network.

Examples

## Not run: 
library(dplyr)
lr_network = readRDS(url("https://zenodo.org/record/3260758/files/lr_network.rds"))
lr_network = lr_network %>% dplyr::rename(ligand = from, receptor = to) %>% dplyr::distinct(ligand, receptor)
sample_id = "tumor"
group_id = "pEMT"
celltype_id = "celltype"
batches = NA
contrasts_oi = c("'High-Low','Low-High'")
senders_oi = SummarizedExperiment::colData(sce)[,celltype_id] %>% unique()
receivers_oi = SummarizedExperiment::colData(sce)[,celltype_id] %>% unique()
celltype_de = perform_muscat_de_analysis(
   sce = sce,
   sample_id = sample_id,
   celltype_id = celltype_id,
   group_id = group_id,
   batches = batches,
   contrasts = contrasts_oi)
sender_receiver_de = combine_sender_receiver_de(
 sender_de = celltype_de$de_output_tidy,
 receiver_de = celltype_de$de_output_tidy,
 senders_oi = senders_oi,
 receivers_oi = receivers_oi,
 lr_network = lr_network)

## End(Not run)

saeyslab/multinichenetr documentation built on Jan. 15, 2025, 7:55 p.m.