Integer copy number matrix output for large sample sets ?

[RodrigoGM]

Hi !
I tested ACE in a data set of 3000+ samples and had a successful run, I really like the figures you have with the absolute copy number predictions. However, I noticed the runACE does not export a table with segment integer copy numbers; is there a way to export this? i.e. on a per-sample basis, have the integer copy number from the best fit exported a table ? Even if it's a text file per sample, these can be combined into a single table with a loop of some sorts.

I have not been able to find this in the documentation; for one or two samples, the manual process is OK, but for a data set of 3000+ samples, it becomes impractical to go one by one.

Thank you, any help would be most appreciated,

[jpoell]

I found out I did not receive notifications for issues on ACE, so I am now dealing with these very old issues. So sorry for that!
Analyzing over 3000 samples means you do not want to go check your fits manually. I think you should only use runACE if you can be quite sure that 2N fits are appropriate for the large majority of your sample. You could switch to looping through the samples and do squaremodel fits. It will take a bit longer, but shouldn't be too bad. Since you are then looping through all samples, you can run getadjustedsegments for each sample and retrieve the segment integer copies from the resulting data frame.