get_expressed_genes - fix for Seurat v5 and add method for matrices

[csangara]

This slightly differs from #247 in that this is no longer true:

• The order of arguments has changed from function(ident, seurat_obj, pct = 0.1, assay_oi = NULL) to function(seurat_obj, ident, assay_oi = NULL, pct = 0.1, ...) because the main object has to be the first argument

The S3Method is now written to dispatch on the second argument to maintain consistency with previous versions. Therefore, the function is still defined as function(celltype_oi, seurat_obj, pct = 0.1, assay_oi = NULL, ...), which will still work with the vignettes.

[codecov-commenter]

Codecov Report

Attention: 97 lines in your changes are missing coverage. Please review.

Comparison is base (0e14cbe) 70.08% compared to head (17d0efd) 69.59%.
Report is 14 commits behind head on master.

Files	Patch %	Lines
R/supporting_functions.R	26.19%	62 Missing ⚠️
R/application_prediction.R	32.69%	35 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #250      +/-   ##
==========================================
- Coverage   70.08%   69.59%   -0.50%     
==========================================
  Files          16       16              
  Lines        5419     5472      +53     
==========================================
+ Hits         3798     3808      +10     
- Misses       1621     1664      +43     

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