I am trying to run DoubletFinder on a seurat object resulting from the integration of various data.
The integrated seurat object have been fully processed:
Normalization and FindVariableFeature pre-integration
ScaleData, RunPCA, FindNeighbors, FindClusters, RunUMAP on the integrated object.
However when I run, paramSweep_v3() function of DoubletFinder gives me an error even though DoubletFinder
is successfully installed and loaded [library(DoubletFinder)
]:
sweep.res.list_pbmc <- paramSweep_v3(data.seurat.filtered, PCs = 1:20, sct = FALSE)
Error in paramSweep_v3(data.seurat.filtered, PCs = 1:20, sct = FALSE) :
could not find function "paramSweep_v3"
How do I get DoubletFinder paramSweep_v3
function to work?
In older versions of DoubletFinder, paramSweep
works for me as shown below;
sweep.res.list_pbmc <- paramSweep(data.seurat.filtered, PCs = 1:20, sct = FALSE)
Nevertheless, you can always download any specific function from the repository and include it in the existing package.