Reference dataset used for testing and demonstration (Seurat with BPCells-backed matrices)

A reference dataset for accute myeloid leukemia was included in this package for demonstration and testing. The data was originally published in Triana et al. 2021. The SCUBA authors downsampled the original Seurat object to use in the package for automated testing, and converted it into other object formats. The cell types provided by Triana et al. were also condensed into 10 generalized cell types to facilitate demonstration of SCUBA visualization capabilities. Details on the operations performed from the original object are provided in this script in the SCUBA manuscript repository.

Usage

AML_BPCells

Format

An object of class Seurat with 462 rows and 250 columns.

Source

The dataset was obtained from the Figshare. For more information on the operations performed on the original object, see the SCUBA manuscript repository.

Details

This object is identical to AML_Seurat, but the counts and data matrices for the RNA and AB assays are stored using BPCells on-disk matrices. The BPCells-backed matrices enable efficient storage and access of large single-cell datasets while maintaining full compatibility with SCUBA's data retrieval functions. The on-disk matrices are stored in the inst/extdata/AML_BPCells/ directory.

Examples

# Object summary
AML_BPCells
#> An object of class Seurat 
#> 659 features across 250 samples within 2 assays 
#> Active assay: RNA (462 features, 462 variable features)
#>  3 layers present: data, counts, scale.data
#>  1 other assay present: AB
#>  2 dimensional reductions calculated: pca, umap

# Summary of metadata variables in object
meta_varnames(AML_BPCells)
#>  [1] "orig.ident"          "nCount_RNA"          "nFeature_RNA"       
#>  [4] "nCount_AB"           "nFeature_AB"         "nCount_BOTH"        
#>  [7] "nFeature_BOTH"       "BOTH_snn_res.0.9"    "seurat_clusters"    
#> [10] "Prediction_Ind"      "BOTH_snn_res.1"      "ClusterID"          
#> [13] "Batch"               "x"                   "y"                  
#> [16] "x_mean"              "y_mean"              "cor"                
#> [19] "ct"                  "prop"                "meandist"           
#> [22] "cDC"                 "B.cells"             "Myelocytes"         
#> [25] "Erythroid"           "Megakaryocte"        "Ident"              
#> [28] "RNA_snn_res.0.4"     "condensed_cell_type"