small_airway {aggregateBioVar} | R Documentation

## Small Airway `SingleCellExperiment` object

### Description

Small airway epithelium single-cell RNA sequencing data subset combined from 7 porcine individuals. Genotypes represent wildtype (Genotype `WT`; n=3) and CFTR-knockout subjects (Genotype `CFTRKO`; n=4) expressing a cystic fibrosis phenotype.
To access cell counts and column metadata:

- counts: `SummarizedExperiment::assay(small_airway, "counts")`

- metadata: `SummarizedExperiment::colData(small_airway)`

Cell types include:

- Secretory cell

- Endothelial cell

- Immune cell

### Usage

    small_airway

### Format

A SingleCellExperiment object with feature counts of 1311 genes (rows) from 2687 individual cells (columns). Features were subset by gene ontology annotation "ion transport" with included child terms ("anion transport", "cation transport", etc.). Includes a count matrix accessed by assay and column metadata accessed by colData. Metadata variables are defined as:

orig.ident

  Biological sample identifier (i.e. subject)

nCount_RNA

  Number of UMIs (i.e. depth/size factor)

nFeature_RNA

  Features with non-zero counts (i.e. identified features)

Genotype

  Sample Genotype ('CF' == cystic fibrosis)

  - WT = non-CF pig

  - CFTRKO = CFTR knockout

Sample

  Airway region of sample

celltype

  Cell type labels

[Package aggregateBioVar version 1.0.0 Index]