Hello all (again), I received a very helpful answer to this question, and would like to pose one more:
Right now I have this script, which is being called from the command line, writing output to two generically named files ("pvalues" and "qvalues") that are named in the script using the line: write(pvalues, file="pvalues", ncol=1) write(adjusted, file="qvalues", ncol=1) However, ideally I would like those two files to have something appended to their names that make them separate from one another, so I can identify which input they went with and so they won't write over each other when I script this into a Perl pipeline that will process many input files, which is my ultimate goal. I know how to do this in Perl, but not R... is there some way I can add another argument on the command line that will get passed to the R.script, like a simple letter code (e.g. "cro"), and then have it append that to the output file names, so they are, for example: "qvalues_cro" and "pvalues_cro"? Thank you very much, Emily On Jan 27, 2013, at 4:34 AM, peter dalgaard <pda...@gmail.com> wrote: > > On Jan 27, 2013, at 08:33 , Emily Sessa wrote: > >> 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 times and it >> worked like a charm. And then, it stopped working. Now, every time I try to >> do this, I get "Read 0 items" as the next line in the terminal window, and >> the output produced by the script is empty, because it's apparently no >> longer reading anything in. I don't think I changed anything in the script; >> it just stopped being able to execute the scan function. Does anyone have >> any idea how to fix this?? I did not have anything else in that scan line >> when it was working before. I've updated R and restarted my computer in the >> hope that it would help, but it hasn't. Any help would be much appreciated. > > I don't see how that would ever work. The 2nd and further args to Rscript are > passed to R and accesible via commandArgs(). There's no way that scan() can > know what the arguments are. It might work with > > Rscript get_q_values.R < LRT_codeml_output > > though. Or you need to arrange explicitly for scan(file=commandArgs(TRUE)[1]). > >> >> -ES >> ______________________________________________ >> R-help@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.