runCxdsBcdsHybrid {singleCellTK} | R Documentation

## Find doublets/multiplets using cxds_bcds_hybrid.

### Description

A wrapper function for cxds_bcds_hybrid. Annotate doublets/multiplets using a binary classification approach to discriminate artificial doublets from original data. Generate a doublet score for each cell. Infer doublets if `estNdbl` is `TRUE`.

### Usage

    runCxdsBcdsHybrid(
      inSCE,
      sample = NULL,
      seed = 12345,
      nTop = 500,
      cxdsArgs = list(),
      bcdsArgs = list(),
      verb = FALSE,
      estNdbl = FALSE,
      force = FALSE,
      useAssay = "counts"
    )

### Arguments

`inSCE` | A SingleCellExperiment object. Needs `counts` in assays slot.
`sample` | Character vector. Indicates which sample each cell belongs to. cxds_bcds_hybrid will be run on cells from each sample separately. If NULL, then all cells will be processed together. Default NULL.
`seed` | Seed for the random number generator. Default 12345.
`nTop` | The number of top varialbe genes to consider. Used in both `csds` and `bcds`. Default `500`.
`cxdsArgs` | See cxds_bcds_hybrid for more information. Default `NULL`.
`bcdsArgs` | See cxds_bcds_hybrid for more information. Default `NULL`.
`verb` | See cxds_bcds_hybrid for more information. Default `FALSE`.
`estNdbl` | See cxds_bcds_hybrid for more information. Default `FALSE`.
`force` | See cxds_bcds_hybrid for more information. Default `FALSE`.
`useAssay` | A string specifying which assay in the SCE to use.

### Value

A SingleCellExperiment object with cxds_bcds_hybrid output appended to the colData slot. The columns include hybrid_score and optionally hybrid_call. Please refer to the documentation of cxds_bcds_hybrid for details.

### Examples

    data(scExample, package = "singleCellTK")
    sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
    sce <- runCxdsBcdsHybrid(sce)

[Package singleCellTK version 2.0.0 Index]