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Quality Control Single-Cell RNA-Seq Dataset

Source: R/dataDocumentation.R
qc_data.Rd

This dataset contains the processed query dataset from the Bunis haematopoietic stem and progenitor cell data. It has been preprocessed to include log-normalized counts, QC metrics, SingleR cell type predictions, and annotation scores.

Usage

qc_data

Format

An object of class SingleCellExperiment with 500 rows and 750 columns.

Source

Bunis DG et al. (2021). Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells Cell Rep. 34(1): 108573

Details

This dataset underwent the following steps:

  • Loads the hpca reference dataset using fetchReference from the celldex package.

  • Loads the QC dataset (Bunis haematopoietic stem and progenitor cell data) from Bunis DG et al. (2021).

  • Adds QC metrics to the QC dataset using the function addPerCellQCMetrics from the scuttle package.

  • Performs log normalization on the QC dataset using the function logNormCounts from the scuttle package.

  • Runs SingleR to predict cell types and assigns predicted labels to the QC dataset using the function SingleR from the SingleR package.

  • Assigns annotation scores to the QC dataset.

  • Selects specific columns (total, SingleR_annotation, annotation_scores) from the cell metadata for downstream analysis.

  • Selects highly variable genes (HVGs) using the function getTopHVGs from the scran package on the QC dataset.

References

Bunis DG et al. (2021). Single-Cell Mapping of Progressive Fetal-to-Adult Transition in Human Naive T Cells Cell Rep. 34(1): 108573

See also

Use data("qc_data") to load and access the resulting quality control dataset.

Examples

# Load and explore the quality control dataset
data("qc_data")