nichenetr (version 0.1.0)

get_active_signaling_network: Get active signaling network in a receiver cell.

Description

get_active_signaling_network Get active signaling network by looking for which signaling-related genes are expressed in the receiver cell. Instead of looking at absolute expression, it is possible as well to extract a signaling network of differentially expressed signaling mediators if a vector of log2 fold change values is used as input.

Usage

get_active_signaling_network(expression_receiver, sig_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

sig_network

A data frame / tibble containing signaling 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 signaling 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_sig_network = get_active_signaling_network(expression_vector_receiver,sig_network,expression_cutoff_receiver = 4)
# }