cxds2 | R Documentation |

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) and making it robust to low sparsity.

```
cxds2(x, whichDbls = c(), ntop = 500, binThresh = NULL)
```

`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. |

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

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

```
sce <- mockDoubletSCE()
sce <- cxds2(sce)
# which is equivalent to
# sce$cxds_score <- cxds2(counts(sce))
```

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