remove_outliers {scPipe} | R Documentation

## Remove outliers in `SingleCellExperiment`

### Description

Removes outliers flagged by `detect_outliers()`

### Usage

    remove_outliers(sce)

### Arguments

`sce` | a `SingleCellExperiment` object

### Value

a `SingleCellExperiment` object without outliers

### Examples

    data("sc_sample_data")
    data("sc_sample_qc")
    sce = SingleCellExperiment(assays = list(counts = as.matrix(sc_sample_data)))
    organism(sce) = "mmusculus_gene_ensembl"
    gene_id_type(sce) = "ensembl_gene_id"
    QC_metrics(sce) = sc_sample_qc
    demultiplex_info(sce) = cell_barcode_matching
    UMI_dup_info(sce) = UMI_duplication
    sce = detect_outlier(sce)
    dim(sce)
    sce = remove_outliers(sce)
    dim(sce)

[Package scPipe version 1.8.0 Index]