KolodziejczykESCData: Obtain the Kolodziejcyzk ESC data

Description Usage Arguments Details Value Author(s) References Examples

View source: R/KolodziejczykESCData.R

Description

Obtain the mouse embryonic stem cell single-cell RNA-seq data from Kolodziejczyk et al. (2015).

Usage

1
KolodziejczykESCData(remove.htseq = TRUE, location = TRUE)

Arguments

remove.htseq

Logical scalar indicating whether HT-seq alignment statistics should be removed.

location

Logical scalar indicating whether genomic coordinates should be returned.

Details

Column metadata is generated from the column names, and contains the culture conditions and the plate of origin for each cell.

Count data for ERCC spike-ins are stored in the "ERCC" 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/kolodziejczyk-esc.

Value

A SingleCellExperiment object with a single matrix of read counts.

Author(s)

Aaron Lun

References

Messmer T et al. (2019). Transcriptional heterogeneity in naive and primed human pluripotent stem cells at single-cell resolution. Cell Rep 26(4), 815-824.e4

Examples

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