This function checks that the spe
object has the appropriate structure.
For more details please check the vignette documentation.
check_spe(
spe,
variables = c("sum_umi", "sum_gene", "expr_chrM", "expr_chrM_ratio")
)
Defaults to the output of
fetch_data(type = 'spe')
. This is a
SpatialExperiment-class
object with the spot-level Visium data and information required for
visualizing the histology. See fetch_data()
for more details.
A character()
vector of variable names expected to
be present in colData(spe)
.
The input object if all checks are passed.
Other Check input functions:
check_modeling_results()
,
check_sce_layer()
,
check_sce()
if (enough_ram()) {
## Obtain the necessary data
if (!exists("spe")) spe <- fetch_data("spe")
## Check the object
check_spe(spe)
}
#> 2023-09-05 20:29:30.071741 loading file /github/home/.cache/R/BiocFileCache/152d33414640_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1
#> class: SpatialExperiment
#> dim: 33538 47681
#> metadata(0):
#> 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(69): sample_id Cluster ... array_row array_col
#> reducedDimNames(6): PCA TSNE_perplexity50 ... TSNE_perplexity80
#> UMAP_neighbors15
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : pxl_col_in_fullres pxl_row_in_fullres
#> imgData names(4): sample_id image_id data scaleFactor