diff --git a/README.md b/README.md index ab52e09..3c8698b 100644 --- a/README.md +++ b/README.md @@ -127,6 +127,46 @@ server <- function(input, output, session) { shinyApp(ui, server) ``` +### Filter Subnetwork by Context + +Use `filterSubnetworkByContext` to filter a subnetwork based on contextual relevance using PubMed abstracts. + +```r +# Example nodes and edges +nodes <- data.frame(id = c("TP53", "MDM2", "CDKN1A")) +edges <- data.frame( + source = c("TP53", "MDM2"), + target = c("MDM2", "TP53"), + interaction = c("Activation", "Inhibition"), + site = c("", ""), + evidenceLink = c("", ""), + stmt_hash = c("", "") +) + +# Define query and filter by context +query <- c("TP53", "DNA damage") +filtered_subnetwork <- filterSubnetworkByContext(nodes, edges, query, cutoff = 1, method = "tag_count") +print(filtered_subnetwork) +``` + +### Delete an Edge from a Network + +Use `deleteEdgeFromNetwork` to remove an edge from the network data frame. + +```r +# Example edges data frame +edges <- data.frame( + source = c("TP53", "MDM2", "CDKN1A"), + target = c("MDM2", "TP53", "TP53"), + interaction = c("Activation", "Inhibition", "Activation"), + stringsAsFactors = FALSE +) + +# Delete an edge +edges <- deleteEdgeFromNetwork(edges, "MDM2", "TP53", "Inhibition") +print(edges) +``` + ## License This package is distributed under the [Artistic-2.0](https://opensource.org/licenses/Artistic-2.0) license. However, its dependencies may have different licenses.