Check input sce

Source: R/check_sce.R

This function checks that the sce object has the appropriate structure. This is a legacy function and we highly encourage you to use SpatialExperiment-class objects and check them with check_spe().

check_sce(
  sce,
  variables = c("GraphBased", "ManualAnnotation", "Maynard", "Martinowich",
    paste0("SNN_k50_k", 4:28), "spatialLIBD", "cell_count", "sum_umi", "sum_gene",
    "expr_chrM", "expr_chrM_ratio", "SpatialDE_PCA", "SpatialDE_pool_PCA", "HVG_PCA",
    "pseudobulk_PCA", "markers_PCA", "SpatialDE_UMAP", "SpatialDE_pool_UMAP", "HVG_UMAP",
    "pseudobulk_UMAP", "markers_UMAP", "SpatialDE_PCA_spatial",
    "SpatialDE_pool_PCA_spatial", "HVG_PCA_spatial", "pseudobulk_PCA_spatial",
    "markers_PCA_spatial", "SpatialDE_UMAP_spatial", "SpatialDE_pool_UMAP_spatial", 
    
    "HVG_UMAP_spatial", "pseudobulk_UMAP_spatial", "markers_UMAP_spatial")
)

Arguments

sce

Defaults to the output of fetch_data(type = 'sce'). This is a SingleCellExperiment object with the spot-level Visium data and information required for visualizing the histology. See fetch_data() for more details.

variables

A character() vector of variable names expected to be present in colData(sce).

Value

The input object if all checks are passed.

See also

Other Check input functions: check_modeling_results(), check_sce_layer(), check_spe()

Examples


if (enough_ram()) {
    ## Obtain the necessary data
    if (!exists("sce_example")) sce_example <- fetch_data("sce_example")

    ## Check the object
    check_sce(sce_example)
}
#> 2024-04-19 19:41:57.754516 loading file /github/home/.cache/R/BiocFileCache/2264419c597_sce_sub_for_vignette.Rdata%3Fdl%3D1
#> class: SingleCellExperiment 
#> dim: 33538 47681 
#> metadata(1): image
#> assays(2): counts logcounts
#> rownames(33538): ENSG00000243485 ENSG00000237613 ... ENSG00000277475
#>   ENSG00000268674
#> rowData names(9): source type ... gene_search is_top_hvg
#> colnames(47681): AAACAACGAATAGTTC-1 AAACAAGTATCTCCCA-1 ...
#>   TTGTTTCCATACAACT-1 TTGTTTGTGTAAATTC-1
#> colData names(74): barcode sample_name ... spatialLIBD ManualAnnotation
#> reducedDimNames(6): PCA TSNE_perplexity50 ... TSNE_perplexity80
#>   UMAP_neighbors15
#> mainExpName: NULL
#> altExpNames(0):