LunSpikeInData: Obtain the Lun spike-in data

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

Obtain the Lun spike-in data

Description

Obtain the spike-in single-cell RNA-seq data from Lun et al. (2017).

Usage

LunSpikeInData(
  which = c("416b", "tropho"),
  split.oncogene = FALSE,
  location = TRUE,
  legacy = FALSE
)

Arguments

which	String specifying whether the 416B or trophoblast data should be obtained.
split.oncogene	Logical scalar indicating whether the oncogene should be split to a separate altExp.
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

Row data contains a single "Length" field describing the total exonic length of each feature.

Column metadata is provided in the same form as supplied in E-MTAB-5522. This contains information such as the cell type, plate of origin, spike-in addition order and oncogene induction.

Two sets of spike-ins were added to each cell in each dataset. These are available as the "SIRV" and "ERCC" entries in the altExps.

If split.oncogene=TRUE and which="416b", the CBFB-MYH11-mcherry oncogene is moved to extra "oncogene" entry in the altExps.

If location=TRUE, the coordinates of the Ensembl gene models are stored in the rowRanges of the output.

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

Value

A SingleCellExperiment object with a single matrix of read counts.

Author(s)

Aaron Lun

References

Lun ATL et al. (2017). Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data. Genome Res. 27(11), 1795-1806.

Examples

sce <- LunSpikeInData()

sce <- LunSpikeInData("tropho")

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