SingleR - "sc_data" is missing

[nitinmahajan20]

I am having issue running the Single R (2.4.1) , 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

[j-andrews7]

See #249. Without sessionInfo(), my guess is this is related to either an old R version, old SingleR version (though you say you're using the most current, so presumably not that), or some issue in a dependency, as sc_data is not found anywhere in the SingleR codebase.