This function checks that the sce_layer object has the appropriate structure.
For more details please check the vignette documentation.
check_sce_layer(sce_layer, variables = "spatialLIBD")Defaults to the output of
fetch_data(type = 'sce_layer'). This is a
SingleCellExperiment
object with the spot-level Visium data compressed via pseudo-bulking to the
layer-level (group-level) resolution. See fetch_data() for more details.
A character() vector of variable names expected to
be present in colData(sce_layer).
The input object if all checks are passed.
Other Check input functions:
check_modeling_results(),
check_sce(),
check_spe()
## Obtain example data from the HumanPilot project
## (Maynard, Collado-Torres, et al, 2021)
if (!exists("sce_layer")) sce_layer <- fetch_data("sce_layer")
#> 2024-10-31 20:25:13.134764 loading file /github/home/.cache/R/BiocFileCache/4a11f72b28f_Human_DLPFC_Visium_processedData_sce_scran_sce_layer_spatialLIBD.Rdata%3Fdl%3D1
## Check the pseudo-bulked data
check_sce_layer(sce_layer)
#> class: SingleCellExperiment
#> dim: 22331 76
#> metadata(0):
#> assays(2): counts logcounts
#> rownames(22331): ENSG00000243485 ENSG00000238009 ... ENSG00000278384
#> ENSG00000271254
#> rowData names(10): source type ... is_top_hvg is_top_hvg_sce_layer
#> colnames(76): 151507_Layer1 151507_Layer2 ... 151676_Layer6 151676_WM
#> colData names(13): sample_name layer_guess ...
#> layer_guess_reordered_short spatialLIBD
#> reducedDimNames(6): PCA TSNE_perplexity5 ... UMAP_neighbors15 PCAsub
#> mainExpName: NULL
#> altExpNames(0):