sc_sample_data {scPipe} | R Documentation

## a small sample scRNA-seq counts dataset to demonstrate capabilities of scPipe

### Description

This data set contains counts for high variable genes for 100 cells. The cells have different cell types. The data contains raw read counts. The cells are chosen randomly from 384 cells and they did not go through quality controls. The rows names are Ensembl gene ids and the columns are cell names, which is the wall position in the 384 plates.

### Usage

    sc_sample_data

### Format

a matrix instance, one row per gene.

### Value

NULL, but makes a matrix of count data

### Author(s)

Luyi Tian

### Source

Christin Biben (WEHI). She FACS sorted cells from several immune cell types including B cells, granulocyte and some early progenitors.

### Examples

    # use the example dataset to perform quality control
    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)

    plot_QC_pairs(sce)

[Package scPipe version 1.6.0 Index]