cyto_setup() Recursive issue

[rwbaer]

Briefly describe what you hope to achieve: I am going through the cyto_setup() process but when I collected my spill standards I collected a couple of samples that I don't want to use in the final process. I therefore created an "unused" subfolder and dumped the extra calibration samples in there. When I run cyto_setup(), it finds the unused folder and apparently doesn't ignore it.

I looked for something like pattern = ".fcs" or recursive = FALSE to help eliminate its chocking but I could not find such a thing. Is there a way to get it to ignore this "unused" subfolder?

Undesirable workaround: If I remove the "unused" folder from the "spill" folder everything proceeds as expected.

Outline the steps taken to attempt to reach this goal (paste code below):

• Include all data preparation steps where appropriate.

  
  > gs <- cyto_setup(path = "./2020-02-29 Phagocytosis(2h)_04/Spill",

• gatingTemplate = "spill.csv",
• restrict = TRUE) Loading FCS files into a GatingSet... Error in fcs_to_cytoset(sapply(files, normalizePath), list(which.lines = which.lines, : can't open the file: D:\RStudioProjects\Phagocytosis\2020-02-29 Phagocytosis(2h)_04\Spill\Unused Please check if the path is normalized to be recognized by c++!

Include any associated screenshots or images here:

[DillonHammill]

See exclude and select arguments for cyto_load() which is called by cyto_setup()

gs <- cyto_setup(path = "./2020-02-29 Phagocytosis(2h)_04/Spill",
                 gatingTemplate = "spill.csv", 
                 restrict = TRUE,
                 exclude = "Unused")

Alternatively,

gs <- cyto_setup(path = "./2020-02-29 Phagocytosis(2h)_04/Spill",
                 gatingTemplate = "spill.csv", 
                 restrict = TRUE,
                 select = ".fcs")

[rwbaer]

Thanks so much. BTW, I did look at ?cyto_setup before posting, including "additional arguments passed to load_cytoset_from_fcs." and didn't find them. I feel badly to keep bothering you, but be assured that I am grateful for your package and your awesome help.