PubMatrix function — PubMatrix • PubMatrixR

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,
  A = NULL,
  B = NULL,
  API.key = NULL,
  Database = "pubmed",
  daterange = NULL,
  outfile = NULL
)

Arguments

file: A file containing search terms. If A and B are NULL, search terms will be read from this file.
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 as a .csv file. If NULL, no file will be exported.

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.