createArrowFiles but with differing filtering criteria

[poorvi4]

To whom it may concern,

Thanks for the wonderful package! I'm trying to automate the process of creating arrow files for any given list of fragment files inputed into my script. I was wondering if it were possible to pass differing minTSS and minFrags criteria corresponding to each fragments file in the inputFiles list? I tried doing this with calling createArrowFiles(...) in lapply for each fragments file and their respective QC criteria but realized this was not feasible given the hdf5 format. Is there a workaround for this aside from explicitly calling the function multiple times for each file?

Once again thank you for the package!

[rcorces]

You could use a standard cutoff, create arrow files, and then for each sample/Arrow File identify the cells you want to keep, keep track of all of those cell names, and then pass them to subsetArchRProject() to create new copies of the Arrow files with only the cells you desire. not sure that helps but other than calling createArrowFiles() individually, I think thats the best way.