This function will filter doublets from an ArchRProject after addDoubletScores() has been run.

filterDoublets(
ArchRProj = NULL,
cutEnrich = 1,
cutScore = -Inf,
filterRatio = 1
)

## Arguments

ArchRProj |
An `ArchRProject` object. |

cutEnrich |
The minimum numeric cutoff for `DoubletEnrichment` . This number is equivalent to the number of simulated
doublets identified as a nearest neighbor to the cell divided by the expected number given a random uniform distribution. |

cutScore |
The minimum numeric cutoff for `DoubletScore` which represents the `-log10(binomial adjusted p-value)` for the `DoubletEnrichment` . |

filterRatio |
The maximum ratio of predicted doublets to filter based on the number of pass-filter cells.
For example, if there are 5000 cells, the maximum would be `filterRatio * 5000^2 / (100000)` (which simplifies to `filterRatio * 5000 * 0.05` ).
This `filterRatio` allows you to apply a consistent filter across multiple different samples that may have different
percentages of doublets because they were run with different cell loading concentrations.
The higher the `filterRatio` , the greater the number of cells potentially removed as doublets. |