doubletThresholding: doubletThresholding

In plger/scDblFinder: scDblFinder

doubletThresholding

Description

Sets the doublet scores threshold; typically called by scDblFinder.

Usage

doubletThresholding(
  d,
  dbr = NULL,
  dbr.sd = NULL,
  dbr.per1k = 0.008,
  stringency = 0.5,
  p = 0.1,
  method = c("auto", "optim", "dbr", "griffiths"),
  perSample = TRUE,
  returnType = c("threshold", "call")
)

Arguments

d	A data.frame of cell properties, with each row representing a cell, as produced by 'scDblFinder(..., returnType="table")', or minimally containing a 'score' column.
dbr	The expected (mean) doublet rate. If 'd' contains a 'cluster' column, the doublet rate will be adjusted for homotypic doublets.
dbr.sd	The standard deviation of the doublet rate, representing the uncertainty in the estimate. Ignored if 'method!="optim"'.
dbr.per1k	The expected proportion of doublets per 1000 cells.
stringency	A numeric value >0 and <1 which controls the relative weight of false positives (i.e. real cells) and false negatives (artificial doublets) in setting the threshold. A value of 0.5 gives equal weight to both; a higher value (e.g. 0.7) gives higher weight to the false positives, and a lower to artificial doublets. Ignored if 'method!="optim"'.
p	The p-value threshold determining the deviation in doublet score.
method	The thresholding method to use, either 'auto' (default, automatic selection depending on the available fields), 'optim' (optimization of misclassification rate and deviation from expected doublet rate), 'dbr' (strictly based on the expected doublet rate), or 'griffiths' (cluster-wise number of median absolute deviation in doublet score).
perSample	Logical; whether to perform thresholding individually for each sample.
returnType	The type of value to return, either doublet calls ('call') or thresholds ('threshold').

Value

A vector of doublet calls if 'returnType=="call"', or a threshold (or vector of thresholds) if 'returnType=="threshold"'.

Examples

sce <- mockDoubletSCE()
d <- scDblFinder(sce, verbose=FALSE, returnType="table")
th <- doubletThresholding(d, dbr=0.05)
th

plger/scDblFinder documentation built on Oct. 19, 2024, 6:26 a.m.