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 <pdalgd@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
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