It's not possible to cover a complex analysis step by step in an answer. I think you should work through a tutorial of the analysis or the R packages you intend to use. Also, to group your samples properly, you need to understand the data first. To do that you need the correct meta-data and again how to get these depends on where you got your data from.

• Are you downloading your data from SRA or ENA or are these new data produced by your lab?

• What kind of data is it (could be sequencing or methylation arrays)?

• Which R-package are you trying to use?

If someone gave you new data, they better explain the grouping of samples to you. Meet with them and tell them you cannot analyze their data unless they provide comprehensive annotation. If you are using public data, you need to read through the meta-data that have been -hopefully- properly deposited, possibly also the connected publication.

If you don't know from the lab/biological site which samples belong to which group then nobody can help you here. This is directly related to the experiment and study design, so you need to talk to your PI or people who performed the experiment to know. Once you have the information one can tell you here how to code that up in R.