Entering edit mode
After performing manual curation (i.e. after creating the manual curation .csv files and editing them to modify the purity and/or ploidy), in order to re-run PureCN.R, which one of these is necessary?
1. Just run PureCN.R the same as before, it will recognize the existence of the curation file and use it.
or
2. Run PureCN.R but specify the --rds argument, giving it the name of the .rds file produced the first time PureCN was run.
or
3. Do readCurationFile() to get a new RDS object, then do saveRDS() to save that object to a new .rds file under a new filename, then run PureCN.R, specifying --rds argument and giving it that new filename.
Regarding 2, do I need to save a new copy of the original .rds file, i.e. like 3 but instead of using a new file name, just use the original .rds name? Or, will PureCN itself take care of changing the .rds file when I do 2?
It won't change the RDS, but this shouldn't be necessary. If you need the RDS in R (outside the command line tools), simply load it with readCurationFile instead of readRDS and you should be fine.