[suggestion] Add outputDir argument to processTSS and determineTSR

[rpolicastro]

Would be handy to have an explicit argument, such as outputDir, to specify where you want the text files to be written if writeTable = TRUE in either processTSS or determineTSR. It's often a little more convenient than having to change the working directory for each of the commands.

[vpbrendel]

I don't know why one would want to change the working directory for each of the commands - that seems to be a very non-R kind of way. All calculations should be done within R on the S4 object, with output to disk an option when needed.

[rpolicastro]

Hi Volker,

Currently when writeTable = TRUE, the text files containing the TSSs and TSRs are written to the current working directory. What this means is if you wanted to write the TSSs or TSRs to a directory other than the current working directory, you need to change directories to the new directory before running the command in R, or move the files after creation. I was suggesting adding an explicit outputDir argument so that instead of having to change directories or move the files, you can specify where you want them to be output to in the first place.

[vpbrendel]

Understood, but again I don't think any of that is necessary. More straightforward would be to move files from the working directory after R is finished, if necessary.