LunSpikeInData: Obtain the Lun spike-in data

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

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
)

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.

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")

drisso/scRNAseq documentation built on Feb. 16, 2021, 1:18 a.m.