Description Usage Arguments Details Value Author(s) References Examples
View source: R/UsoskinBrainData.R
Obtain the mouse brain single-cell RNA-seq dataset from Usoskin et al. (2015).
1 | UsoskinBrainData(ensembl = FALSE, location = TRUE)
|
ensembl |
Logical scalar indicating whether the output row names should contain Ensembl identifiers. |
location |
Logical scalar indicating whether genomic coordinates should be returned. |
Column metadata is provided in the same form as supplied in External Table 2 of http://linnarssonlab.org/drg/. This contains information such as the library of origin and the cell type.
The count matrix contains information for repeats, marked with r_
prefixes in the row names;
as well as mitochondrial transcripts, marked with mt-
prefixes.
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/usoskin-brain
.
A SingleCellExperiment object with a single matrix of RPMs.
Aaron Lun
Usoskin A et al. (2015). Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. Nat. Neurosci. 18(1), 145-53.
1 | sce <- UsoskinBrainData()
|
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