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dviraran / SingleR

SingleR: Single-cell RNA-seq cell types Recognition (legacy version)
GNU General Public License v3.0
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SingleR - "sc_data" is missing #160

Open nitinmahajan20 opened 3 months ago

nitinmahajan20 commented 3 months ago

I am having issue running the Single R , not sure why I am getting the error. Please help

seurat_integrated

An object of class Seurat 51866 features across 54453 samples within 3 assays Active assay: RNA (24468 features, 0 variable features) 2 layers present: data, counts 2 other assays present: SCT, integrated 2 dimensional reductions calculated: pca, umap

ref <- celldex::HumanPrimaryCellAtlasData()
seurat_integrated_counts <- GetAssayData(seurat_integrated, layer = 'counts')

pred <- SingleR(test = seurat_integrated_counts,
        ref = ref,
        labels = ref$label.main)

pred

ERROR

Error in SingleR(test = seurat_integrated_counts, ref = ref, labels = ref$label.main) :  argument "sc_data" is missing, with no default
dviraran commented 3 months ago

Please post issues in LTLA/SingleR