Ranks the genes mediating each focal-neighbour relationship by driver score,
populating topDrivers(). Requires paceShrink() and paceDecompose() to
have run first.
Usage
paceDrivers(object, ...)
# S4 method for class 'PACEFit'
paceDrivers(object, spe = NULL, pairs = NULL, ...)Arguments
- object
A PACEFit with shrunken slopes and a decomposition.
- ...
Unused.
- spe
The SpatialExperiment::SpatialExperiment that was fitted. Needed only for an older fit that stores neither its fitted means nor their per-cell-type statistics.
- pairs
Optional list of focal-neighbour pairs to score;
NULLscores all pairs.
Details
The driver scores read each cell type's mean fitted mean, which the fit
stores. For an older fit saved without its fitted means or those statistics
they are rebuilt exactly from the fit and spe, as in paceDecompose(), a
block of genes at a time; pass spe for such a fit.
Examples
spe <- readRDS(system.file("extdata", "bc_xenium_subset.rds", package = "PACE"))
fit <- readRDS(system.file("extdata", "pace_fit_example.rds", package = "PACE"))
fit <- paceDrivers(fit, spe)
names(topDrivers(fit))
#> [1] "B_Cell_Dendritic_Cell" "B_Cell_Endothelial"
#> [3] "B_Cell_Macrophage" "B_Cell_Myoepithelial"
#> [5] "B_Cell_Stromal" "B_Cell_T_Cell"
#> [7] "B_Cell_Tumour" "Dendritic_Cell_B_Cell"
#> [9] "Dendritic_Cell_Endothelial" "Dendritic_Cell_Macrophage"
#> [11] "Dendritic_Cell_Myoepithelial" "Dendritic_Cell_Stromal"
#> [13] "Dendritic_Cell_T_Cell" "Dendritic_Cell_Tumour"
#> [15] "Endothelial_B_Cell" "Endothelial_Dendritic_Cell"
#> [17] "Endothelial_Macrophage" "Endothelial_Myoepithelial"
#> [19] "Endothelial_Stromal" "Endothelial_T_Cell"
#> [21] "Endothelial_Tumour" "Macrophage_B_Cell"
#> [23] "Macrophage_Dendritic_Cell" "Macrophage_Endothelial"
#> [25] "Macrophage_Myoepithelial" "Macrophage_Stromal"
#> [27] "Macrophage_T_Cell" "Macrophage_Tumour"
#> [29] "Myoepithelial_B_Cell" "Myoepithelial_Dendritic_Cell"
#> [31] "Myoepithelial_Endothelial" "Myoepithelial_Macrophage"
#> [33] "Myoepithelial_Stromal" "Myoepithelial_T_Cell"
#> [35] "Myoepithelial_Tumour" "Stromal_B_Cell"
#> [37] "Stromal_Dendritic_Cell" "Stromal_Endothelial"
#> [39] "Stromal_Macrophage" "Stromal_Myoepithelial"
#> [41] "Stromal_T_Cell" "Stromal_Tumour"
#> [43] "T_Cell_B_Cell" "T_Cell_Dendritic_Cell"
#> [45] "T_Cell_Endothelial" "T_Cell_Macrophage"
#> [47] "T_Cell_Myoepithelial" "T_Cell_Stromal"
#> [49] "T_Cell_Tumour" "Tumour_B_Cell"
#> [51] "Tumour_Dendritic_Cell" "Tumour_Endothelial"
#> [53] "Tumour_Macrophage" "Tumour_Myoepithelial"
#> [55] "Tumour_Stromal" "Tumour_T_Cell"