sc_sample_qc: quality control information for a small sample scRNA-seq...

In LuyiTian/scPipe: Pipeline for single cell multi-omic data pre-processing

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.

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")

LuyiTian/scPipe documentation built on Dec. 11, 2023, 8:21 p.m.