Closed klai001 closed 7 months ago
Hi!
For Seurat objects, try extracting the 'misc' data using the code data.integrated@misc$CHOIR
instead. The Misc()
function doesn't work for this.
The CHOIR-computed PCA reductions will be under data.integrated@misc$CHOIR$reduction
. The primary PCA reduction can also be found under data.integrated@reductions$CHOIR_P0_reduction
.
CHOIR does not automatically compute UMAP reductions. To do so, please run the runCHOIRumap()
function.
Thanks for trying CHOIR!
thanks! i got it
thank you for the nice package, i managed to run it- however i would like to extract the PCs and UMAPs coordinates which CHOIR runs to store in the reduction slots of the seurat object. i tried Misc(data.integrated, slot=Integrated) and Misc(data.integrated, slot=RNA) which you mentioned in the tutorial but everything is NULL. here's my code snippet before running CHOIR, i stored it in integrated data slot
thanks