I am working on analyzing cytof data for my lab and while I have successfully been able to use the gui method as well as the step by step command option, I am having an issue with saving files once I have completed the analysis.
I need help accessing the csv files after performing an analysis using commands. I do not have trouble with the files being sent to the directory if using the gui option, however when I am using the command option of cytofkit, I cannot successfully save R.data or any csv files.
I am using the "cytof_writeResults" function and when it saves into the directory, there is only one csv file and it does not contain any information once I open it. Furthermore, the R.data file crashes the Shiny APP. I have set the "saveToFCS" value to false as I have already been able to save an FCS file and when I set it to true, I get this error:
Error in do.call(cbind, dimReducedData) : second argument must be a list
Is the cytof_writeResults function not working because I did not use the cytof function directly?
I like being able to use the commands so I can have more flexibility with my results so any help would be appreciated.
Thanks in advance,