get_active_regulatory_network: Get active gene regulatory network in a receiver cell.

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

Get active gene regulatory network in a receiver cell.

Description

get_active_regulatory_network Get active regulatory network by looking for which TFs/regulatory genes are expressed in the receiver cell. Instead of looking at absolute expression, it is possible as well to extract a gene regulatory network of differentially expressed TFs if a vector of log2 fold change values is used as input.

Usage

get_active_regulatory_network(expression_receiver, gr_network, expression_cutoff_receiver = 0)

Arguments

expression_receiver	A named numeric vector of gene expression levels (absolute or logfc) for the receiver cell that receives extracellular signals from the sender cell
gr_network	A data frame / tibble containing gene regulatory interactions (required columns: from, to). Can be both unweighted and weighted.
expression_cutoff_receiver	The cutoff on expression value for the receiver cell: receptors will be considered active if their expression is higher than the cutoff. Default: 0.

Value

A data frame containing at least the variables from, to, receiver_expression. In this network, the active gene regulatory interactions in the system of interest are shown.

Examples

## Not run: 
library(dplyr)
expression_vector_receiver = rnorm(n = 10000, mean = 6, sd = 3)
names(expression_vector_receiver) = sample(x = geneinfo_human$symbol,size = 10000,replace = FALSE)
receiver_gr_network = get_active_regulatory_network(expression_vector_receiver,gr_network,expression_cutoff_receiver = 4)

## End(Not run)

saeyslab/nichenetr documentation built on March 26, 2024, 9:22 a.m.