combine_summary: Combine PubMed and STRING Metrics

In DeSciDe: Tool for Unbiased Literature Searching and Gene List Curation

Combine PubMed and STRING Metrics

Description

Combine PubMed search summary and STRING gene metrics.

Usage

combine_summary(
  pubmed_search_results,
  string_results,
  file_directory = NULL,
  export_format = "csv",
  export = FALSE,
  threshold_percentage = 20
)

Arguments

pubmed_search_results	Data frame with PubMed search results.
string_results	Data frame with STRING metrics.
file_directory	Directory for saving the output summary. Defaults to NULL.
export_format	Format for export, either "csv", "tsv", or "excel".
export	Logical indicating whether to export the summary. Defaults to FALSE.
threshold_percentage	Percentage threshold for ranking (default is 20%).

Value

A data frame with combined summary including connectivity, precedence, and category.

Examples

pubmed_data <- data.frame(Gene = c("Gene1", "Gene2"), PubMed_Rank = c(1, 2))
string_data <- data.frame(Gene = c("Gene1", "Gene2"), Connectivity_Rank = c(2, 1))
combined <- combine_summary(pubmed_data, string_data, export = FALSE)
print(combined)

DeSciDe documentation built on Sept. 1, 2025, 1:08 a.m.