Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Compatibility issues of DoubletFinder 2.0.4 with Seurat V4 #192

Open
zhongguozhiwang opened this issue Feb 17, 2024 · 1 comment
Open

Compatibility issues of DoubletFinder 2.0.4 with Seurat V4 #192

zhongguozhiwang opened this issue Feb 17, 2024 · 1 comment

Comments

@zhongguozhiwang
Copy link

Hello, may I ask if the new version of DoubletFinder can not be used in Seurat V4? I have an error when using it. Is there a good solution if I do not update Seurat?
Thank you!
`

packageVersion('Seurat')
[1] ‘4.4.0’
packageVersion('DoubletFinder')
[1] ‘2.0.4’

all.list <- lapply(X = all.list, FUN = function(x) {
sweep.res.list <- paramSweep(x, PCs = 1:20, sct = FALSE)
sweep.stats <- summarizeSweep(sweep.res.list, GT = FALSE)
bcmvn <- find.pK(sweep.stats)
pK <- bcmvn$pK[which.max(bcmvn$BCmetric)] %>% as.character() %>% as.numeric()
DoubletRate <- ncol(x)/100000.06
homotypic.prop <- modelHomotypic(x$seurat_clusters)
nExp_poi <- round(DoubletRate
nrow(x@meta.data))
nExp_poi.adj <- round(nExp_poi*(1-homotypic.prop))
x <- doubletFinder(x, PCs = 1:20, pN = 0.25, pK = pK, nExp = nExp_poi.adj, reuse.pANN = FALSE, sct = FALSE)
})

Error in seu@assays$RNA$counts : $ operator not defined for this S4 class
`

@Drizzle63
Copy link

I find this, you can use it try to solve this problem. remotes::install_github('lzmcboy/DoubletFinder_204_fix')
I have the same version of Seurat and DoubletFinder with you,but I find that :
Error in seu@meta.data : no applicable method for @ applied to an object of class "list"
so I want to know if you would have this problem too

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants