cell_barcode_matching {scPipe} | R Documentation |
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
sc_sample_qc
a data.frame instance, one row per cell.
NULL, but makes a data frame with cell barcode demultiplex statistics
Luyi Tian
Christin Biben (WEHI). She FACS sorted cells from several immune cell types including B cells, granulocyte and some early progenitors.
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)