2.3 Create project space

The project space created by scMINER is a folder of specified name in specified directory. It contains 4 subfolders:

  • DATA: to save the sparse eSet objects and other files;
  • MICA: to save the inputs and outputs of mutual information-based clustering analysis;
  • SJARACNe: to save the inputs and outputs of network inference and quality control;
  • PLOT: to save the files of data visualization.

The project space can not only keep your data centralized and organized, but also make the scMINER pipeline more smooth and robust. We strongly recommend you to create a project space for each of your studies.

This can be easily done by createProjectSpace() in scMINER:

scminer_dir <- createProjectSpace(project_dir = "/your-path", project_name = "PBMC14k")

The command above will create a folder named PBMC14k in /your-path, and save the path to the project space (/your-path/PBMC14k) to scminer_dir.

Can I add, delete or modify files in project space folder?

Yes, you can.

  • There are two functions, drawNetworkQC() and getActivityBatch(), that take directories as inputs, and both of them can validate the inputs. For all the rest functions, the inputs are specific files. So adding files in project space never affect the scMINER analysis.
  • Deleting or modifying files in project spare is also safe. The input validation features of scMINER functions can help locate the files with issues. All output files of scMINER are reproducible and can be re-generated quickly. Just be careful with the clustering results in MICA and network files in SJARACNe, ad regerating them can take some time.