sc_sample_qc {scPipe} | R Documentation

## quality control information for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe.

### Description

This data.frame contains cell quality control information for the 100 cells. For each cell it has:

- unaligned the number of unaligned reads.

- aligned_unmapped the number of reads that aligned to genome but fail to map to any features.

- mapped_to_exon is the number of reads that mapped to exon.

- mapped_to_intron is the number of reads that mapped to intron.

- ambiguous_mapping is the number of reads that mapped to multiple features. They are not considered in the following analysis.

- mapped_to_ERCC is the number of reads that mapped to ERCC spike-in controls.

- mapped_to_MT is the number of reads that mapped to mitochondrial genes.

- total_count_per_cell is the number of reads that mapped to exon after UMI deduplication. In contrast, 'mapped_to_exon' is the number of reads mapped to exon before UMI deduplication.

- number_of_genes is the number of genes detected for each cells

- non_ERCC_percent is 1 - (percentage of ERCC reads). Reads are UMI deduplicated.

- non_mt_percent is 1 - (percentage of mitochondrial reads). Reads are UMI deduplicated.

- non_ribo_percent is 1- (percentage of ribosomal reads). Reads are UMI deduplicated.

### Usage

    sc_sample_qc

### Format

a data.frame instance, one row per cell.

### Value

NULL, but makes a data frame with cell quality control data.frame

### 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

    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
    head(QC_metrics(sce))
    plot_mapping(sce,percentage=TRUE,dataname="sc_sample")

[Package scPipe version 1.4.1 Index]