Reduces a solution network based on a decoupling analysis of upstream and downstream gene expression, by filtering out edges that do not meet a consistency threshold, and limiting the network to a certain number of steps from upstream input nodes.
Usage
reduce_solution_network(
decoupleRnival_res,
meta_network,
cutoff,
upstream_input,
RNA_input = NULL,
n_steps = 10
)Arguments
- decoupleRnival_res
A data frame resulting from the decoupleRnival function.
- meta_network
A network data frame containing signed directed prior knowledge of molecular interactions.
- cutoff
The consistency threshold for filtering edges from the solution network.
- upstream_input
A named vector with up_stream nodes and their corresponding activity.
- RNA_input
A named vector containing differential gene expression data.
- n_steps
The maximum number of steps from upstream input nodes to include in the solution network.
Value
A list containing the solution network (SIF) and an attribute table (ATT) with gene expression data.
Examples
# Example input data
upstream_input <- c("A" = 1, "B" = -1, "C" = 0.5)
downstream_input <- c("D" = 2, "E" = -1.5)
meta_network <- data.frame(
source = c("A", "A", "B", "C", "C", "D", "E"),
target = c("B", "D", "D", "E", "D", "B", "A"),
interaction = c(-1, 1, -1, 1, -1, -1, 1)
)
RNA_input <- c("A" = 1, "B" = -1, "C" = 5, "D" = 0.7, "E" = -0.3)
# Run the decoupleRnival function to get the upstream influence scores
upstream_scores <- decoupleRnival(upstream_input, downstream_input, meta_network, n_layers = 2, n_perm = 100)
#> [1] "Warning, this function is deprecated and will no longer receive futur support. Please use the 'moon' function instead"
# Reduce the solution network based on the upstream influence scores
reduced_network <- reduce_solution_network(upstream_scores, meta_network, 0.4, upstream_input, RNA_input, 3)
#> [1] "COSMOS: removing nodes that are not reachable from inputs within 3 steps"
#> [1] "COSMOS: 0 from 4 interactions are removed from the PKN"
# View the resulting solution network and attribute table
print(reduced_network$SIF)
#> source target interaction consistency
#> 1 A B -1 TRUE
#> 2 A D 1 TRUE
#> 3 B D -1 TRUE
#> 6 D B -1 TRUE
print(reduced_network$ATT)
#> nodes score RNA_input
#> 1 A 1.05659 1.0
#> 2 B -1.05659 -1.0
#> 3 D 2.00000 0.7