View source: R/application_network_extraction.R
get_active_signaling_network | R Documentation |
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.
get_active_signaling_network(expression_receiver, sig_network, expression_cutoff_receiver = 0)
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. |
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.
## 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)
## End(Not run)
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