scmap icon indicating copy to clipboard operation
scmap copied to clipboard

How should I import data from seurat to scmap?

Open jsonProgram opened this issue 3 years ago • 0 comments

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!

jsonProgram avatar Aug 11 '21 07:08 jsonProgram