Per-gene variance decomposition

Returns the per-gene, per-focal variance decomposition. By default the observed single-frame decomposition (cell-type identity, spatial cell state, contamination, residual; and a responder spatial block for condition cohorts) is returned; set which = "blocks" for the underlying link-scale block tables.

Usage

varianceDecomposition(object, ...)

# S4 method for class 'PACEFit'
varianceDecomposition(object, which = c("perGene", "blocks"), ...)

Arguments

object

A PACEFit.

...

Unused.

which

Either "perGene" (default, the observed single-frame table) or "blocks" (the raw link-scale decomposition).

Value

A data frame (for "perGene") or a list (for "blocks").

Examples

fit <- readRDS(system.file("extdata", "pace_fit_example.rds", package = "PACE"))
head(varianceDecomposition(fit))
#>          focal    gene Cell type %    Spatial % Spillover % Residual %
#> SEC11C  B_Cell  SEC11C  18.7147181 14.494678932   0.6373641   66.15324
#> DAPK3   B_Cell   DAPK3  14.5989691  0.002760858   1.0526045   84.34567
#> TCIM    B_Cell    TCIM  85.9791365  0.002251981   0.5945541   13.42406
#> NKG7    B_Cell    NKG7   0.3900736  0.002239134   8.2668800   91.34081
#> RAPGEF3 B_Cell RAPGEF3  14.2060602  0.008126525   3.2152159   82.57060
#> PPARG   B_Cell   PPARG   9.2327061  0.013567627   4.4774151   86.27631
#>           SS_lineage  SS_within      denom n_focal
#> SEC11C   638.5745510 2773.57704 3412.15159     330
#> DAPK3     14.4759924   84.68164   99.15763     330
#> TCIM    2153.2706156  351.13999 2504.41061     330
#> NKG7       0.3704028   94.58676   94.95716     330
#> RAPGEF3   37.1808640  224.54451  261.72537     330
#> PPARG     31.1183156  305.92605  337.04436     330