Calculates a coexpression-based doublet score using the method developed by Bais and Kostka 2020. This is the original implementation from the scds package, but enabling scores to be calculated for all cells while the gene coexpression is based only on a subset (i.e. excluding known/artificial doublets) and making it robust to low sparsity.
Usage
cxds2(x, whichDbls = c(), ntop = 500, binThresh = NULL)Arguments
- x
A matrix of counts, or a `SingleCellExperiment` containing a 'counts'
- whichDbls
The columns of `x` which are known doublets.
- ntop
The number of top features to keep.
- binThresh
The count threshold to be considered expressed.
Value
A cxds score or, if `x` is a `SingleCellExperiment`, `x` with an added `cxds_score` colData column.
Examples
sce <- mockDoubletSCE()
sce <- cxds2(sce)
# which is equivalent to
# sce$cxds_score <- cxds2(counts(sce))