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:

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 1.2.1 Index]