Question: PureCN Manual Curation .rds file
0
gravatar for twtoal
13 months ago by
twtoal0
twtoal0 wrote:

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.

 

ADD COMMENTlink modified 13 months ago by markus.riester110 • written 13 months ago by twtoal0
Answer: PureCN Manual Curation .rds file
1
gravatar for markus.riester
13 months ago by
markus.riester110 wrote:

2 is what I do. PureCN.R will load readCurationFile and will then regenerate all the output files. 1 won't work. 3 will work, but the additional step is not necessary. 

ADD COMMENTlink written 13 months ago by markus.riester110

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?

 

ADD REPLYlink written 13 months ago by twtoal0

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.

ADD REPLYlink written 13 months ago by markus.riester110
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 129 users visited in the last hour