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kstreet13 / slingshot

Functions for identifying and characterizing continuous developmental trajectories in single-cell data.
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How do I extract feature_info in my rds file? #242

Open Saumya513 opened 5 months ago

Saumya513 commented 5 months ago

I want to do a trajectory analysis using slingshot on my seurat object. But the function feature_mapper that is created uses feature_info. How do I extract this from my seurat object?

Any help will be appreciated?

kstreet13 commented 5 months ago

Hi @Saumya513,

Thanks for the question! In order to run Slingshot, you will first need to convert your Seurat object into a SingleCellExperiment object using the function as.SingleCellExperiment. There is no way to run Slingshot directly on a Seurat object.

Best, Kelly

Saumya513 commented 5 months ago

Dear Kelly, I tried to run

lineages <- getLineages(data = dimred, clusterLabels = clustering)

I was getting this error:

Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.

I'd appreciate your help.

Thanks and regards, Saumya Gupta

On Tue, Jan 30, 2024 at 3:15 AM Kelly Street @.***> wrote:

Hi @Saumya513 https://github.com/Saumya513,

Thanks for the question! In order to run Slingshot, you will first need to convert your Seurat object into a SingleCellExperiment object using the function as.SingleCellExperiment. There is no way to run Slingshot directly on a Seurat object.

Best, Kelly

— Reply to this email directly, view it on GitHub https://github.com/kstreet13/slingshot/issues/242#issuecomment-1915627762, or unsubscribe https://github.com/notifications/unsubscribe-auth/A4HQMNY733OVEESFRZGXJELYRAKBPAVCNFSM6AAAAABCO3CBEWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJVGYZDONZWGI . You are receiving this because you were mentioned.Message ID: @.***>

kstreet13 commented 5 months ago

This is probably a result of having a few out-of-date packages installed. You can run BiocManager::install() to update any installed Bioconductor packages and you may also need to update (re-install) the Matrix and matrixStats packages.

Saumya513 commented 5 months ago

Thanks, I'll check it out.

On Sat, 10 Feb 2024, 07:24 Kelly Street, @.***> wrote:

This is probably a result of having a few out-of-date packages installed. You can run BiocManager::install() to update any installed Bioconductor packages and you may also need to update (re-install) the Matrix and matrixStats packages.

— Reply to this email directly, view it on GitHub https://github.com/kstreet13/slingshot/issues/242#issuecomment-1936807336, or unsubscribe https://github.com/notifications/unsubscribe-auth/A4HQMNYYRNFPWPCXQYWNYALYS3HM7AVCNFSM6AAAAABCO3CBEWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMZWHAYDOMZTGY . You are receiving this because you were mentioned.Message ID: @.***>