Frequently asked questions / problems with the code

[derrik-gratz]

General questions

• I can't load a library

Check to see if the library is installed. You can try sourcing the helper scripts '0#_install_packages.R' to try installing all
needed dependencies for that session. Depending on the version of R you have installed, other packages you have installed,
your machine/OS, etc., these helper scripts may not cover all dependencies you need. If you get error messages trying to
install packages through R studio, try reading the error messages and see if other dependencies are missing. You may need to install system libraries, which are handled outside of R.

• I can't load the data

Filepaths in the provided scripts rely on a project-based workflow using the here library to establish relative paths to the project directory. If you rename any files or folders, the paths may no longer be valid. You may need to edit the path to point to the directory on your machine, and you may need to remove the here() command if you aren't using a R-project workflow.

Session 03 - QC, filtering, clustering

• My script stops at the 'Construct neighbor graph' section

A few lines in this script have prompts for your input. This is to practice the decision making you will do on real data. Replace the '???' with appropriate values

sig_dims <- ???    ## <- Replace the '???' with an integer based on the elbow plot
obj <- FindNeighbors(obj, dims = 1:sig_dims)
obj@graphs$RNA_snn[1:6, 1:6]