cxds2: cxds2

Description Usage Arguments Value Examples

View source: R/misc.R

Description

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).

Usage

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cxds2(x, whichDbls = c(), ntop = 500, binThresh = 0)

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

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2
sce <- mockDoubletSCE()
sce <- cxds2(sce)

scDblFinder documentation built on Nov. 8, 2020, 5:48 p.m.