The results of the previous commands are simply reported on the shell of R and they aren't saved in any format in my working directory. How can I save these results? And which format should I use to save them?
Each step in ChAMP pipeline should generate a R object, which could be list, dataframe, vector. etc. You can save it like a normal R objects like save(myLoad, file="myLoad.RData"), then you can reload them anytime you want.
However, it's not easy to save them into a "easy to open" format like Excel, txt, because as I said there are lists, dataframe, vectors in it. Personally I suggest people firstly check what are these returned result via R, like using head() function, and read manual. Then for some key results, for example dataframe result from champ.DMP(), you may save it into Excel like: write_xls(myDMP[], "DMPExcelTable.xlsx")