writeChatGPTqueryDEG — writeChatGPTqueryDEG • Giotto

This function writes a query as a .txt file that can be used with ChatGPT or a similar LLM service to find the most likely cell types based on the top differential expressed genes (DEGs) between identified clusters.

writeChatGPTqueryDEG(
  DEG_output,
  top_n_genes = 10,
  tissue_type = "human breast cancer",
  folder_name = getwd(),
  file_name = "chatgpt_query.txt"
)

Arguments

DEG_output: the output format from the differenetial expression functions
top_n_genes: number of genes for each cluster
tissue_type: tissue type
folder_name: path to the folder where you want to save the .txt file
file_name: name of .txt file

Value

writes a .txt file to the desired location

Details

This function does not run any LLM service. It simply creates the .txt file that can then be used any LLM service (e.g. OpenAI, Gemini, ...)