doubletPairwiseEnrichment {scDblFinder} | R Documentation

## 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)

[Package scDblFinder version 1.8.0 Index]