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Hsu-Che-Wei / COPILOT

Single cell RNA-seq preprocessing tool for gene-by-cell matrices of UMI counts. It is recommended to use the raw spliced and unpliced counts matrices produced by scKB pipeline as the input of copilot.
MIT License
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Some errors in ipynb file #8

Open landa04 opened 1 year ago

landa04 commented 1 year ago

Hi Hsu-Che-Wei! I am using the COPILOT pipeline, but I have a little problem with the ipynb format file, in the "1-Correlation_Based_Annotation" file in the ln[18] some lines can't be copied

The correct code are like these?

Store the annotation, correlation coefficient and the p-value in Seurat object

seu@meta.data$celltype.ID.P <- as.character(celltype_ident) seu@meta.data$timezone.ID.P <- as.character(time_ident) seu@meta.data$celltype.cor.P <- celltype_max seu@meta.data$timezone.cor.P <- time_max seu@meta.data$celltype.pvalue.P <- celltype_maxp seu@meta.data$timezone.pvalue.P <- time_maxp

In case there is cell with insufficient information for annotation, label them as "unknown"

seu@meta.data$celltype.ID.P[which(seu@meta.data$celltype.ID.P=='character(0)')]="unknown" seu@meta.data$timezone.ID.P[which(seu@meta.data$timezone.ID.P=='character(0)')]="unknown"

Best!

Hsu-Che-Wei commented 1 year ago

Yes, you are right. I don't know why the codes are off.

Thank you for pointing it out!

Best, Che-Wei