Update paramSweep.R

[Camila-goclowski]

recieve error: "$ operator not defined for this S4 class" when previously trying to run paramSweep function.
Change:
seu@assays$RNA@counts
instead of
seu@assays$RNA$counts made this work

[jennieli421]

Hi, Is this issue resolved? I installed doubletfinder yesterday and was experiencing this error:

> paramSweep(s, PCs = 1:10, sct = FALSE)
Error in seu@assays$RNA$counts : $ operator not defined for this S4 class

However when I try to update doubletfinder, it seems like I'm already on the newest version

> remotes::install_github('chris-mcginnis-ucsf/DoubletFinder')
Using github PAT from envvar GITHUB_PAT
Skipping install of 'DoubletFinder' from a github remote, the SHA1 (853e2de1) has not changed since last install.
  Use `force = TRUE` to force installation

[Camila-goclowski]

@jennieli421 I was having the same issue, I think the error is new with the recent update. I grabbed the function code from the github page, corrected the error (in two locations for paramSweep() and one for doubletFinder()), and manually created my "own" function to run the analysis. Hope that helps and I imagine the package itself will be updated soon with the correction.

[RoseString]

Will it be easier to use getAssayData(seu, assay = 'RNA', slot = 'counts') to avoid future code change due to different Seurat versions?

[Camila-goclowski]

@RoseString Very good point, I agree

with Seurat's layer organization I was able to get this to run smoothly by using GetAssayData(seu, layer = "counts") which seemed to work