cell_barcode_matching: cell barcode demultiplex statistics for a small sample...

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

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)

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