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

tidyseurat::aggregate_cells doesn't pull all meta.data columns of Seurat object? #81

Open
denvercal1234GitHub opened this issue Jan 9, 2024 · 4 comments

Comments

@denvercal1234GitHub
Copy link

Hi there,

Thanks for a great tool.

tidyseurat::aggregate_cells only pull some but not all metadata columns of the original Seurat object.

Would you mind taking a look?

Thank you again.

seuratObj %>% tidyseurat::aggregate_cells(.sample = c(Leiden39PCRes1p2_clusterID_2024Jan09), assays = "SCT", slot = "data", aggregation_function=Matrix::rowSums) |> filter(.feature %in% gene_vector) -> seuratObj_Data

> ncol(seuratObj_Data)
[1] 25
> ncol([email protected])
[1] 92
@stemangiola
Copy link
Owner

stemangiola commented Jan 9, 2024

Hello,

Only metadata columns relative to samples and features are pulled. the ones about cells do not fit bulk data anymore.

@william-hutchison could you please add a message to the aggregate_cells of tidyseurat and tidySCE communicating this?

Only for tidyseurat also add a second message that says that you can then use tidySE to convert to SE with the code ..

Please @denvercal1234GitHub confirm that such message is very understandable by you. Otherwise please propose an alternative.

@denvercal1234GitHub
Copy link
Author

The comment that tidyseurat::aggregate_cells only pull sample-level and feature-level metadata columns but not cell-level columns" makes sense.

But, I am confused about the conversion to SE using tidySE? What is it for?

Thank you both.

@stemangiola
Copy link
Owner

actually is tidybulk::as_SummarizedExperiment

you want SE if you do bulk analyses for example. many tools including tidybulk accept SE

@denvercal1234GitHub
Copy link
Author

I see. tidybulk is to analyze bulk-RNAseq data and not scRNAseq data.

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