Filter Doublets From an ArchRProject — filterDoublets • ArchR

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.