MairPBMCData: Obtain the Mair CITE-seq data

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

Obtain the Mair CITE-seq data

Description

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

Usage

MairPBMCData(
  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

Column metadata contains the donor identity and cartridge of origin. Some libraries may also be classified as multiplets or have undeterminate origins after hash tag debarcoding.

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/mair-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

Mair C et al. (2020). A targeted multi-omic analysis approach measures protein expression and low-abundance transcripts on the single-cell level. Cell Rep. 31, 107499

Examples

sce <- MairPBMCData()

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