diff --git a/vignettes/articles/seurat_to_celda_pbmc3k.Rmd b/vignettes/articles/seurat_to_celda_pbmc3k.Rmd index 418dad20..54f3ac03 100644 --- a/vignettes/articles/seurat_to_celda_pbmc3k.Rmd +++ b/vignettes/articles/seurat_to_celda_pbmc3k.Rmd @@ -107,15 +107,11 @@ reducedDim(sce, "factorizeMatrix") <- t(factorizedLogcounts) sce <- runFindMarker(sce, useReducedDim = "factorizeMatrix", cluster = "seurat_clusters", useAssay = NULL) ``` -The differential expression results are contained within `sce@metadata$findMarker`. The `Gene` column denotes the differentially expressed module, whilst the `Log2_FC` column denotes the level of upregulation of the module in the cluster. These results can be accessed through the `getFindMarkerTopTable` function. - -```{r, eval = FALSE} -getFindMarkerTopTable(sce) -``` +The differential expression results are contained within the metadata slot `findMarker`. The `Gene` column denotes the differentially expressed module, whilst the `Log2_FC` column denotes the level of upregulation of the module in the cluster. ```{r DE module table, message=FALSE, echo = FALSE} -kable(sce@metadata$findMarker, style = "html", row.names = FALSE) %>% +kable(metadata(sce)$findMarker, style = "html", row.names = FALSE) %>% kable_styling(bootstrap_options = "striped") %>% scroll_box(width = "100%", height = "500px") ```