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saeyslab · Oct 20, 2023 · ff76e11 · ff76e11
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diff --git a/vignettes/seurat_steps_prioritization.Rmd b/vignettes/seurat_steps_prioritization.Rmd
@@ -147,7 +147,6 @@ prioritizing_weights = c("de_ligand" = 1,
 We provide helper functions to calculate these values, including `calculate_de` and `get_exprs_avg`. `process_table_to_ic` transforms these different dataframes so they are compatible with the `generate_prioritization_tables` function.
 
 ```{r}
-celltypes <- unique(seuratObj$celltype)
 lr_network_renamed <- lr_network %>% rename(ligand=from, receptor=to)
 
 # Only calculate DE for LCMV condition, with genes that are in the ligand-receptor network

diff --git a/vignettes/seurat_steps_prioritization.md b/vignettes/seurat_steps_prioritization.md
@@ -231,7 +231,6 @@ these different dataframes so they are compatible with the
 `generate_prioritization_tables` function.
 
 ``` r
-celltypes <- unique(seuratObj$celltype)
 lr_network_renamed <- lr_network %>% rename(ligand=from, receptor=to)
 
 # Only calculate DE for LCMV condition, with genes that are in the ligand-receptor network