satijalab / seurat

R toolkit for single cell genomics

http://www.satijalab.org/seurat

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Mixscape eccite$NT typo error? #8578

Closed strawberry098 closed 5 months ago

strawberry098 commented 6 months ago

In the mixscape vignette, eccite$NT is not present in the Seurat object metadata table. Is there a typo?

Calculate percentage of KO cells for all target gene classes.

df <- prop.table(table(eccite$mixscape_class.global, eccite$NT),2)

longmanz commented 5 months ago

Hi, Can you provide your sessionInfo() of your Seurat and SeuratData package? Testing from my end, we can see the "NT" column is present in the eccite@meta.data (see below): Screen Shot 2024-03-15 at 2 17 46 PM

strawberry098 commented 5 months ago

@longmanz

I'm using a dataset from an arrayed CRISPR experiment rather than a pooled screen. After renaming my control sample as "NT", I was able to follow through with the analysis. Thank you!