LedergorMyelomaData: Obtain the Ledergor Myeloma data

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

Obtain the Ledergor Myeloma data

Description

Obtain the human multiple myeloma single-cell RNA-seq data from Ledergor et al. (2018).

Usage

LedergorMyelomaData(ensembl = FALSE, location = TRUE, legacy = FALSE)

Arguments

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 was created from the sample metadata file in GSE117156. It contains an 'Experiment_ID' column, from which the tissue and subject of origin were extracted, as well as the condition and treatment status of the subject.

If ensembl=TRUE, the gene symbols 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 of the output. 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/ledergor-myeloma.

Value

A SingleCellExperiment object with a single matrix of read counts.

Author(s)

Milan Malfait

References

Ledergor G et al. (2018) Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma. Nat Med. 24(12), 1867–1876.

Examples

sce <- LedergorMyelomaData()

LTLA/scRNAseq documentation built on June 28, 2024, 7:31 p.m.