Possible to split samples into groups after initial processing?

We have run DNA and cDNA sequences from patients, controls and 3 different locations. The samples are named like this: DNA_P_11111_1c (DNA_patient_sample number_location). Our bioinformatichian is new in the game and has processed the samples through to MiSeq SOP. My question is if it is possible to arange the data in groups at this point- making trees showing a selection of the samples etc. Or do samples need to be split in a way from the very start. I’ve tried different ways removing.groups etc my self, but I don’t seem to be able to make group files that are valid.
I would be extremely happy to get any input on how to organize our data!!

Have you tried get.groups and remove.groups?