scrubDoublets: The main function used to identify doublets
In ChengxiangQiu/rscrublet: Remove doublets from single-cell RNA-seq data set

Description Usage Arguments Value

The main function used to identify doublets

scrubDoublets(exp, n_neighbors = NULL, doublet_score_threshold = NULL,
  sim_doublet_ratio = 2, expected_doublet_rate = 0.06,
  stdev_doublet_rate = 0.02, synthetic_doublet_umi_subsampling = 1,
  use_approx_neighbors = TRUE, distance_metric = "euclidean",
  min_counts = 2, min_cells = 3, min_gene_variability_pctl = 85,
  log_transform = FALSE, z_score = TRUE, n_prin_comps = 30,
  verbose = TRUE)

`exp`	expression matrix of a single-cell RNA-seq data set (gene, cell)
`n_neighbors`	the number of neighbors used to create the KNN graph
`doublet_score_threshold`	the threshold used to separate doublets
`sim_doublet_ratio`	the expected doublet ratio
`stdev_doublet_rate`	the standard deviation of doublet rate
`synthetic_doublet_umi_subsampling`	the subsampling rate while simulation
`use_approx_neighbors`	whether use approx neighbors
`distance_metric`	which method use measure distance of two nodes
`min_counts`	minimum read count of cell
`min_cells`	minimum detected cell of gene
`min_gene_variability_pctl`	minumum gene variability percentage
`log_transform`	whether perform log transformation
`z_score`	whether transfer to z_score
`n_prin_comps`	the number of prin comps used
`verbose`	whether display processing message