build a XenSCE instance based on the SFEData XeniumOutput element

build_panc_subset(cache = BiocFileCache::BiocFileCache())

Arguments

cache: BiocFileCache::BiocFileCache() is default

Note

This builds a XenSCE instance with on-disk counts. `data(panc_sub)` retrieves an instance with counts in dgCMatrix format, in memory.

Examples

panc_sub_h5 = build_panc_subset()
panc_sub_h5
#> class: XenSCE 
#> dim: 514 6272 
#> metadata(0):
#> assays(1): counts
#> rownames(514): ENSG00000121270 ENSG00000130234 ...
#>   UnassignedCodeword_0497 UnassignedCodeword_0499
#> rowData names(1): symbol
#> colnames(6272): abclkehb-1 abcnopgp-1 ... odmgoega-1 odmgojlc-1
#> colData names(12): cell_id x_centroid ... nucleus_area sample_id
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : x_centroid y_centroid
#> imgData names(0):
#> Geometry elements:
#>               nrow ncol
#> transcripts 367354   11
#> cellbounds  156512    4
#> nucbounds   154156    4