cxds {scds} | R 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)

[Package scds version 1.8.0 Index]