search for: lrt_codeml_output

Hi all, I am trying to use the scan function in an R script that I am calling from the command line on a Mac; at the shell prompt I type: $ Rscript get_q_values.R LRT_codeml_output in the hope that LRT_codeml_output will get passed to the get_q_values R script. The first line of that script is: chidata <- scan(file="") which, as I understand how scan works, will read the contents of the file from the command line into the object chidata. I did this a few tim...