Returns, for each cell type, the genes used as negative-control anchors when identifying the per-cell contamination loading: genes owned by another cell type (high mean expression there) that are near-absent in the focal type. Anchors are recomputed with the same selection as the fit, and ranked by expression in their owning cell type. This is the source of the manuscript's supplementary anchor-gene tables.
Arguments
- object
A PACEFit (supplies the cell-type and image columns used at fit time).
- spe
The SpatialExperiment::SpatialExperiment that was fitted.
- top_n
Number of top anchors to list per cell type (default 10).
- assay_name
Counts assay name (default
"counts").
Value
A data frame with one row per cell type: cellType, n_anchors
(total anchors), and top_anchors (the top_n strongest, comma-separated).
Examples
spe <- readRDS(system.file("extdata", "bc_xenium_subset.rds", package = "PACE"))
fit <- readRDS(system.file("extdata", "pace_fit_example.rds", package = "PACE"))
anchorGenes(fit, spe)
#> anchors: homotypic-core cells 5168/7898; anchors/type median=136 range=[129,149]
#> Warning: NAs introduced by coercion
#> cellType n_anchors
#> 1 B_Cell 129
#> 2 Dendritic_Cell 141
#> 3 Endothelial 129
#> 4 Macrophage 136
#> 5 Myoepithelial 136
#> 6 Stromal 131
#> 7 T_Cell 149
#> 8 Tumour 141
#> top_anchors
#> 1 ERBB2, KRT7, POSTN, ANKRD30A, FOXA1, EPCAM, SCD, GATA3, CCND1, MLPH
#> 2 ERBB2, KRT7, ANKRD30A, FOXA1, EPCAM, SCD, GATA3, CCND1, MLPH, FASN
#> 3 ERBB2, KRT7, ANKRD30A, FOXA1, EPCAM, SCD, GATA3, MLPH, FASN, TACSTD2
#> 4 ERBB2, KRT7, ANKRD30A, FOXA1, EPCAM, SCD, GATA3, CCND1, MLPH, FASN
#> 5 POSTN, ANKRD30A, FOXA1, LUM, SCD, MLPH, FASN, CXCR4, TCIM, LYZ
#> 6 KRT7, ANKRD30A, FOXA1, EPCAM, SCD, GATA3, CCND1, MLPH, FASN, TACSTD2
#> 7 ERBB2, KRT7, POSTN, ANKRD30A, FOXA1, EPCAM, SCD, GATA3, CCND1, MLPH
#> 8 POSTN, LUM, MYLK, SERPINA3, KRT14, KRT5, LYZ, KRT6B, VWF, PECAM1