KotliarovPBMCData: Obtain the Kotliarov CITE-seq data

In LTLA/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

Obtain the Kotliarov CITE-seq data

Description

Obtain the Kotliarov PBMC CITE-seq data from Kotliarov et al. (2020).

Usage

KotliarovPBMCData(
  mode = c("rna", "adt"),
  ensembl = FALSE,
  location = TRUE,
  legacy = FALSE
)

Arguments

mode	Character vector specifying whether to return either or both the RNA and ADT counts.
ensembl	Logical scalar indicating whether the output row names should contain Ensembl identifiers.
location	Logical scalar indicating whether genomic coordinates should be returned.
legacy	Logical scalar indicating whether to pull data from ExperimentHub. By default, we use data from the gypsum backend.

Details

This dataset contains 20 samples from 2 experimental batches, where each batch contains 5 high and 5 low responders. The 10 samples per batch were mixed and distributed across the 6 lanes using a cell hashing approach.

The column metadata contains the following fields:

• sample*: identifiers for the sample of origin for each cell.

• adjmfc.time: type of responder for each sample.

• tenx_lane: 10X lane from which each cell was collected.

• batch: the batch of origin.

• barcode_check: barcode identifier.

• hash_* and hto_* columns: HTOdemux outputs.

• DEMUXLET.* columns: demuxlet outputs.

• joint_classification_global: HTOdemux and demuxlet joint classification.

• nGene: number of genes as defined from Seurat's CreateSeuratObject.

• nUMI: number of UMIs as defined from Seurat's CreateSeuratObject.

• pctMT: percent of mitochondrial reads as defined from Seurat's CreateSeuratObject.

Note, no filtering has been performed based on the quality control metrics.

If ensembl=TRUE, the gene symbols in the RNA data are converted to Ensembl IDs in the row names of the output object. Rows with missing Ensembl IDs are discarded, and only the first occurrence of duplicated IDs is retained.

If location=TRUE, the coordinates of the Ensembl gene models are stored in the rowRanges for the RNA data. Note that this is only performed if ensembl=TRUE.

All data are downloaded from ExperimentHub and cached for local re-use. Specific resources can be retrieved by searching for scRNAseq/kotliarov-pbmc.

Value

A SingleCellExperiment object with a single matrix of UMI counts corresponding to the first mode, with an optional alternative Experiment if there is a second mode.

Author(s)

Stephany Orjuela, with modifications from Aaron Lun

References

Kotliarov et al. (2020). Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus. Nat. Med. 26, 618–629

Examples

sce <- KotliarovPBMCData()

LTLA/scRNAseq documentation built on April 24, 2024, 5:58 p.m.