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How should I import data from seurat to scmap? #32

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jsonProgram opened this issue Aug 11, 2021 · 0 comments
Open

How should I import data from seurat to scmap? #32

jsonProgram opened this issue Aug 11, 2021 · 0 comments

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@jsonProgram
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hello ,Vladimir Kiselev and Martin Hemberg

I got error for this code:

SAMPLE <- Seurat::Read10X("./00_Data/Sample_matrix_10X/")
sce <- SingleCellExperiment::SingleCellExperiment(assays=list(counts= SAMPLE ))
seur <- Seurat::CreateSeuratObject(SAMPLE )
sce <- Seurat::as.SingleCellExperiment(seur)
sce <- scater::logNormCounts(sce)
rowData(sce)$feature_symbol <- rownames(sce)

#Feature selection
sce <- scmap::selectFeatures(sce, suppress_plot = FALSE)

##error
sce <- indexCluster(sce)
Error in scmap::indexCluster(sce) :
Please define an existing cluster column of the colData slot of the input object using the cluster_col parameter!

Thanks a lot!

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