check_sce: Check input sce

In LieberInstitute/spatialLIBD: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved transcriptomics data

Check input sce

Description

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().

Usage

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)
}

LieberInstitute/spatialLIBD documentation built on Nov. 4, 2024, 11:57 a.m.