Returns the driver-score tables ranking the genes that mediate each focal-neighbour spatial relationship.
Arguments
- object
A PACEFit.
- ...
Unused.
Value
A named list with one entry per focal-neighbour pair, each a list
with scores (the driver table), status, expected_false_sign and
false_sign_rate.
Details
Each pair's genes are called at lfsr < 0.05. The lfsr is the posterior
probability that a call has the wrong sign, so its sum over a pair's calls,
expected_false_sign, is the expected number of those calls with the wrong
sign, and false_sign_rate is that count as a fraction of the calls
(Stephens 2017). Read a pair's call count against it: many ordered pairs are
tested, and a pair with three calls and an expected 1.5 wrong is weak
evidence. Both are only as well calibrated as the lfsr itself.
On a fit with a condition, the table carries two different slopes and they
are not a raw-and-shrunken pair of the same quantity. b_clean and lfsr
are the condition-interaction term, the one the shrinkage was applied to, and
the driver score is built from b_clean. u_raw is the baseline
slope, the unshrunken BLUP for the neighbour on its own, and it is there
because the variance split needs it: V_S comes from u_raw and V_RxS
from b_clean. On a fit without a condition there is no interaction to
separate, so u_raw is absent and b_clean is the only slope.
Examples
fit <- readRDS(system.file("extdata", "pace_fit_example.rds", package = "PACE"))
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"