An S4 class to store multi-bandwidth spiDE results

Container for one or more SpiDEFit objects (one per niche bandwidth) plus the cross-bandwidth combined inference and the tidy results table produced by testSpiDE().

Usage

# S4 method for class 'SpiDEResults'
x$name

Arguments

x

an object of class SpiDEResults.

name

a character, the slot to retrieve.

Value

Return value varies depending on method.

Slots

fits

a list of SpiDEFit objects, one per bandwidth.

sigma

a numeric, the bandwidth grid.

condition

a character, the condition (colData column) tested; NA_character_ in "niche" mode.

mode

a character, the design mode: "condition" or "niche". In "niche" mode condition is NA_character_ and the results.celltype / results.patient tables are empty.

index

a character, the index cell types considered.

niche

a character, the niche cell types considered.

covariates

a character, the nuisance covariates included.

coldata

a DataFrame of sample-level metadata.

gene.weights

a matrix of per-gene Cauchy-combination weights (genes x bandwidth).

p.cauchy.pos

a matrix, Cauchy-combined up-regulation p-values.

p.cauchy.neg

a matrix, Cauchy-combined down-regulation p-values.

results

a data.frame, the tidy results table (empty until testSpiDE() is run), keyed by (gene, ct_index, ct_niche, bandwidth).

results.celltype

a data.frame of cell-type-specific response calls keyed by (gene, ct_index), from the CellType:condition block. Empty unless the design carries that block. Retrieved with results(object, type = "celltype").

results.patient

a data.frame of patient-level response calls, one abundance-weighted contrast per gene. Empty unless the design carries the CellType:condition block. Retrieved with results(object, type = "patient").

diagnostics

a list of two-stage diagnostic tables (r2, inclusion, tau2); empty for the GLM path.

fdr

a numeric, the FDR threshold used.

call

the matched call that produced the object.