Comments (3)
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.
from tsrchitect.
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.
from tsrchitect.
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.
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Related Issues (11)
- Known issue with assignment of chromosome name to tsrData output HOT 1
- Demo produces unexpected number of slots in @tssCountDataMerged and @tsrDataMerged HOT 3
- [suggestion] bed file of TSRs. HOT 1
- [suggestion] Sample sheet to input experiment information. HOT 1
- [suggestion] bedgraph file for TSSs HOT 1
- Many of the TSR attributes are undocumented. HOT 1
- processTSS using large amounts of memory HOT 5
- mergeSampleData behavior and speed for TSSs HOT 3
- Allow sample sheet to also be a data.frame for input.
- maintenance
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