This function takes two vectors A and B, an API key, a database name, and performs a search operation on the specified database using the search terms from A and B. It then generates a dataframe of search results and optionally exports it as a .csv file. Use plot_pubmatrix_heatmap() to visualize the results as a heatmap.
Usage
PubMatrix(
file = NULL,
A = NULL,
B = NULL,
API.key = NULL,
Database = "pubmed",
daterange = NULL,
outfile = NULL,
export_format = NULL
)Arguments
- file
A file containing search terms (optional). If NULL, search terms will be read from A and B vectors.
- A
A vector of search terms to be paired with B. If NULL, search terms will be read from the file.
- B
A vector of search terms to be paired with A. If NULL, search terms will be read from the file.
- API.key
An API key obtained from Entrez; not necessary.
- Database
Either 'pubmed' or 'pmc'. Determines the database to search.
- daterange
A range of dates to search if desired. Should be a vector of two elements: the start and end date.
- outfile
A file path to export the search dataframe with hyperlinks. If NULL (default), no file will be exported. Ignored if export_format is not specified.
- export_format
Format for exporting the hyperlinked dataframe with clickable links. Options are: NULL (default, no export), 'csv', or 'ods'. When NULL, only returns the dataframe to R without saving. 'csv' exports as Excel-compatible format with HYPERLINK formulas; 'ods' exports as OpenDocument Spreadsheet format compatible with LibreOffice/OpenOffice. Requires outfile parameter when not NULL.
Value
A dataframe of search results. Each element of the dataframe is the number of search results for a pair of search terms from A and B.
Examples
# Note: This example requires internet connection
A <- c("WNT1", "WNT2")
B <- c("FZD1", "FZD2")
# result <- PubMatrix(A = A, B = B, Database = "pubmed", daterange = c(2020, 2023))
# print(result)
message("Example commented out to avoid internet dependency in checks")
#> Example commented out to avoid internet dependency in checks