cell_barcode_matching {scPipe} | R Documentation

## cell barcode demultiplex statistics for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe

### Description

This data.frame contains cell barcode demultiplex statistics with several rows:

- barcode_unmatch_ambiguous_mapping is the number of reads that do not match any barcode, but aligned to the genome and mapped to multiple features.

- barcode_unmatch_mapped_to_intron is the number of reads that do not match any barcode, but aligned to the genome and mapped to intron.

- barcode_match is the number of reads that match the cell barcodes

- barcode_unmatch_unaligned is the number of reads that do not match any barcode, and not aligned to the genome

- barcode_unmatch_aligned is the number of reads that do not match any barcode, but aligned to the genome and do not mapped to any feature

- barcode_unmatch_mapped_to_exon is the number of reads that do not match any barcode, but aligned to the genome and mapped to the exon

### Usage

    sc_sample_qc

### Format

a data.frame instance, one row per cell.

### Value

NULL, but makes a data frame with cell barcode demultiplex statistics

### 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
    demultiplex_info(sce) = cell_barcode_matching
    UMI_dup_info(sce) = UMI_duplication

    demultiplex_info(sce)

[Package scPipe version 1.2.1 Index]