cxds2 {scDblFinder} | R Documentation

## cxds2

### Description

Calculates a coexpression-based doublet score using the method developed by Bais and Kostka 2020. This is the original implementation from the scds package, but enabling scores to be calculated for all cells while the gene coexpression is based only on a subset (i.e. excluding known/artificial doublets).

### Usage

    cxds2(x, whichDbls = c(), ntop = 500, binThresh = 0)

### Arguments

`x` | A matrix of counts, or a 'SingleCellExperiment' containing a 'counts'
`whichDbls` | The columns of 'x' which are known doublets.
`ntop` | The number of top features to keep.
`binThresh` | The count threshold to be considered expressed.

### Value

A cxds score or, if 'x' is a 'SingleCellExperiment', 'x' with an added 'cxds_score' colData column.

### References

https://doi.org/10.1093/bioinformatics/btz698

### Examples

    sce <- mockDoubletSCE()
    sce <- cxds2(sce)

[Package scDblFinder version 1.8.0 Index]