Extract the tidy spiDE results table
Usage
results(object, ...)
# S4 method for class 'SpiDEResults'
results(object, type = c("niche", "celltype", "patient"), ...)Arguments
- object
a SpiDEResults object.
- ...
ignored; present for compatibility with the generic.
- type
which response result to return. "niche" (default) gives the neighbourhood-dependent calls keyed by (gene, ct_index, ct_niche, bandwidth), gated by the 3-level gene -> index -> niche cascade. "celltype" gives cell-type-specific response calls keyed by (gene, ct_index), gated by a 2-level gene -> cell type cascade. "patient" gives one abundance-weighted response contrast per gene. The latter two are empty unless the design carries a CellType:condition block — in particular they are always empty for a condition-free (
condition = NULL) fit, where "niche" instead reports the two-wayCellType:nicheassociations.All three layers combine evidence across every bandwidth, using the same log-likelihood-weighted Cauchy combination. The CellType:condition coefficients are not identical between bandwidths – they are fitted alongside different niche columns – so each bandwidth contributes its own evidence about the same contrast, and combining is what pools it.
Value
a data.frame of significant calls; see type. Empty until
testSpiDE() is run.
Examples
data(toySpiDE)
spe <- buildNiches(toySpiDE, sigma = 20)
res <- spiDE(spe, condition = "condition", sigma = 20, random = "none", verbose = FALSE)
head(results(res))
#> gene ct_index ct_niche bandwidth.max coef t DirectionGene
#> 1 G11 C B 20 88.952901 53.321979 Both
#> 2 G11 B A 20 29.157918 17.500218 Both
#> 3 G17 C B 20 34.709419 13.878225 Up
#> 4 G5 C A 20 21.886440 11.807649 Up
#> 5 G9 C B 20 17.358199 7.341270 Up
#> 6 G1 A B 20 3.205271 5.458804 Up
#> DirectionIndex DirectionNiche fdr.gene fdr.index fdr.niche
#> 1 Up Up 3.996803e-14 2.997602e-15 1.998401e-15
#> 2 Up Up 3.996803e-14 2.997602e-15 1.998401e-15
#> 3 Up Up 3.996803e-14 5.995204e-15 1.998401e-15
#> 4 Up Up 3.996803e-14 5.995204e-15 1.998401e-15
#> 5 Up Up 6.347145e-12 1.269318e-12 4.232170e-13
#> 6 Up Up 1.150443e-06 2.876110e-07 9.587034e-08