remove_outliers: Remove outliers in 'SingleCellExperiment'

In scPipe: pipeline for single cell RNA-seq data analysis

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)

scPipe documentation built on Nov. 8, 2020, 8:28 p.m.