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")
)
A
SpatialExperiment-class
object. See fetch_data()
for how to download some example objects or
read10xVisiumWrapper()
to read in spaceranger --count
output files and
build your own spe
object.
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()
,
check_sce_layer()
if (enough_ram()) {
## Obtain the necessary data
if (!exists("spe")) spe <- fetch_data("spe")
## Check the object
check_spe(spe)
}
#> 2024-12-13 19:40:05.136147 loading file /github/home/.cache/R/BiocFileCache/103d2e431726_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