DeSciDe (version 1.0.2)

descide: Run DeSciDe pipeline

Description

Run the entire analysis pipeline including PubMed search, STRING database search, and plotting.

Usage

descide(
  genes_list,
  terms_list,
  rank_method = "weighted",
  species = 9606,
  network_type = "full",
  score_threshold = 400,
  threshold_percentage = 20,
  export = FALSE,
  file_directory = NULL,
  export_format = "csv"
)

Value

A list containing the PubMed search results, STRING results, and summary results.

Arguments

genes_list

A list of gene IDs.

terms_list

A list of search terms.

rank_method

The method to rank pubmed results, either "weighted" or "total". Weighted ranks results based on order of terms inputted. Total ranks results on total sum of publications across all search term combinations. Defaults to "weighted".

species

The NCBI taxon ID of the species. Defaults to 9606 (Homo sapiens).

network_type

The type of string network to use, either "full" or "physical". Defaults to "full".

score_threshold

The minimum score threshold for string interactions. Defaults to 400.

threshold_percentage

Percentage threshold for ranking (default is 20%).

export

Logical indicating whether to export the results. Defaults to FALSE.

file_directory

Directory for saving the output files. Defaults to NULL.

export_format

Format for export, either "csv", "tsv", or "excel".

Examples

# \donttest{
genes <- c("TP53", "BRCA1")
terms <- c("cancer", "tumor")
results <- descide(genes, terms, export = FALSE)
str(results)
# }