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.

Examples


# Get Test ArchR Project
proj <- getTestProject()

# Add Doublet Scores for Small Project
proj <- addDoubletScores(proj, dimsToUse = 1:5, LSIParams = list(dimsToUse = 1:5, varFeatures=1000, iterations = 2))

# Filter Doublets (Since Low Cells filterRatio has to be high before removing 1 cell!)
proj <- filterDoublets(proj, filterRatio=10)