doubletPairwiseEnrichment: doubletPairwiseEnrichment

In plger/scDblFinder: scDblFinder

doubletPairwiseEnrichment

Description

Calculates enrichment in any type of doublet (i.e. specific combination of clusters) over random expectation. Note that when applied to an multisample object, this functions assumes that the cluster labels match across samples.

Usage

doubletPairwiseEnrichment(
  x,
  lower.tail = FALSE,
  sampleWise = FALSE,
  type = c("poisson", "binomial", "nbinom", "chisq"),
  inclDiff = TRUE,
  verbose = TRUE
)

Arguments

x	A table of double statistics, or a SingleCellExperiment on which scDblFinder was run using the cluster-based approach.
lower.tail	Logical; defaults to FALSE to test enrichment (instead of depletion).
sampleWise	Logical; whether to perform tests sample-wise in multi-sample datasets. If FALSE (default), will aggregate counts before testing.
type	Type of test to use.
inclDiff	Logical; whether to regress out any effect of the identification difficulty in calculating expected counts
verbose	Logical; whether to output eventual warnings/notes

Value

A table of significances for each combination.

Examples

sce <- mockDoubletSCE()
sce <- scDblFinder(sce, clusters=TRUE, artificialDoublets=500)
doubletPairwiseEnrichment(sce)

plger/scDblFinder documentation built on March 20, 2024, 9:46 p.m.