find_in_pubmed: find_in_pubmed

In mgerault/mineCETSAapp: A shiny app for IMPRINTS.CETSA package

find_in_pubmed

Description

Function to check if there is already some publications in Pubmed on your subject. If so, export word files of the publications

Usage

find_in_pubmed(
  data,
  feat = "PI3K",
  imp_by_hitlist = FALSE,
  treatment = "",
  language = NULL,
  year_rg = NULL,
  your_API = NULL,
  save_word = TRUE,
  newfolder_name = "PI3K_pubmed_search"
)

Arguments

data	The word you want to search a publication on. It can be a file path, a character vector, a list or the dataframe hitlist output from the hitlist function.
feat	A second word that will be match to every word from data, can be NULL.
imp_by_hitlist	Logical to tell if the data are in the hitlist format.
treatment	A character vector for selecting specific treatment. Use when data are in hitlist format.
language	A character to tell if you want to select publications in a specific language like 'english'.
year_rg	A character to tell a range of year of publication. The format is '2000:2023'
your_API	A character that is your NCBI API key. If you don't have an account, use NULL.
save_word	A logical to tell if you want to save each publication found (title and abstract) in a word file for each query.
newfolder_name	The name of the folder that will be created for saving the word documents

Value

Dataframe which contains the proteins and if they give a result or not

See Also

hitlist and pmApi2df for more details

Examples

library(IMPRINTS.CETSA.app)
find_in_pubmed("Lamin B1", imp_by_hitlist = FALSE)

mgerault/mineCETSAapp documentation built on April 17, 2025, 7:24 p.m.