cxds_bcds_hybrid: Find doublets/multiples in UMI scRNA-seq data;

In kostkalab/scds: In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data

Find doublets/multiples in UMI scRNA-seq data;

Description

Annotates doublets/multiplets using the hybrid approach

Usage

cxds_bcds_hybrid(sce, cxdsArgs = NULL, bcdsArgs = NULL, verb = FALSE,
  estNdbl = FALSE, force = FALSE)

Arguments

sce	single cell experiment (SingleCellExperiment) object to analyze; needs counts in assays slot.
cxdsArgs	list, arguments for cxds function in list form. Default: NULL
bcdsArgs	list, arguments for bcds function in list form. Default: NULL
verb	logical, switch on/off progress messages
estNdbl	logical, should the numer of doublets be estimated from the data. Enables doublet calls. Default:FALSE. Use with caution.
force	logical, force a (re)run of cxds and bcds. Default: FALSE

Value

sce input sce object SingleCellExperiment with doublet scores added to colData as "hybrid_score" column.

Examples

data("sce_chcl")
## create small data set using only 100 cells
sce_chcl_small = sce_chcl[, 1:100]
sce_chcl_small = cxds_bcds_hybrid(sce_chcl_small)

kostkalab/scds documentation built on Oct. 4, 2022, 6:56 p.m.