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

View source: R/cxds.R

cxdsR Documentation

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.