cxds: Find doublets/multiplets in UMI scRNA-seq data;

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

Find doublets/multiplets in UMI scRNA-seq data;

Description

Annotates doublets/multiplets using co-expression based approach

Usage

cxds(sce, ntop = 500, binThresh = 0, verb = FALSE, retRes = FALSE,
  estNdbl = FALSE)

Arguments

sce	single cell experiment (SingleCellExperiment) object to analyze; needs counts in assays slot.
ntop	integer, indimessageing number of top variance genes to consider. Default: 500
binThresh	integer, minimum counts to consider a gene "present" in a cell. Default: 0
verb	progress messages. Default: FALSE
retRes	logical, whether to return gene pair scores & top-scoring gene pairs? Default: FALSE.
estNdbl	logical, should the numer of doublets be estimated from the data. Enables doublet calls. Default:FALSE. Use with caution.

Value

sce input sce object SingleCellExperiment with doublet scores added to colData as "cxds_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(sce_chcl_small)

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