This function cleans up a meta network data frame by removing self-interactions, calculating the mean interaction values for duplicated source-target pairs, and keeping only interactions with values of 1 or -1.
Examples
# Create a meta network data frame
example_meta_network <- data.frame(
source = c("A", "B", "C", "D", "A", "B", "C", "D", "A"),
interaction = c(1, 1, 1, -1, 1, -1, 1, -1, 1),
target = c("B", "C", "D", "A", "C", "D", "A", "B", "B")
)
# Clean up the example meta network
cleaned_meta_network <- meta_network_cleanup(example_meta_network)
#> Warning: `summarise_each()` was deprecated in dplyr 0.7.0.
#> ℹ Please use `across()` instead.
#> ℹ The deprecated feature was likely used in the cosmosR package.
#> Please report the issue at <https://github.com/saezlab/COSMOSR/issues>.
#> Warning: `funs()` was deprecated in dplyr 0.8.0.
#> ℹ Please use a list of either functions or lambdas:
#>
#> # Simple named list: list(mean = mean, median = median)
#>
#> # Auto named with `tibble::lst()`: tibble::lst(mean, median)
#>
#> # Using lambdas list(~ mean(., trim = .2), ~ median(., na.rm = TRUE))
#> ℹ The deprecated feature was likely used in the cosmosR package.
#> Please report the issue at <https://github.com/saezlab/COSMOSR/issues>.
print(cleaned_meta_network)
#> source target interaction
#> 1 A B 1
#> 2 A C 1
#> 3 B C 1
#> 4 B D -1
#> 5 C A 1
#> 6 C D 1
#> 7 D A -1
#> 8 D B -1