Retrieves published example datasets stored in SingleCellExperiment using the scRNAseq and TENxPBMCData packages. See 'Details' for a list of available datasets.
importExampleData(
dataset,
class = c("Matrix", "matrix"),
delayedArray = FALSE,
rowNamesDedup = TRUE
)
Character. Name of the dataset to retrieve.
Character. The class of the expression matrix stored in the SCE
object. Can be one of "Matrix"
or "matrix"
. "Matrix"
will store the data as a sparse matrix from package Matrix while
"matrix"
will store the data in a standard matrix. Default
"Matrix"
.
Boolean. Whether to read the expression matrix as
DelayedArray object or not. Default FALSE
.
Boolean. Whether to deduplicate rownames. Default
TRUE
.
The specified SingleCellExperiment object.
See the list below for the available datasets and their descriptions.
Retrieved with
ReprocessedFluidigmData
. Returns a dataset of 65
human neural cells from Pollen et al. (2014), each sequenced at high and low
coverage (SRA accession SRP041736).
Retrieved with
ReprocessedAllenData
. Returns a dataset of 379 mouse
brain cells from Tasic et al. (2016).
Retrieved with
NestorowaHSCData
. Returns a dataset of 1920 mouse
haematopoietic stem cells from Nestorowa et al. 2015
Retrieved with TENxPBMCData
.
2,700 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.
Retrieved with TENxPBMCData
.
4,340 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.
Retrieved with TENxPBMCData
.
5,419 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.
Retrieved with TENxPBMCData
.
8,381 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.
Retrieved with TENxPBMCData
.
33,148 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.
Retrieved with TENxPBMCData
.
68,579 peripheral blood mononuclear cells (PBMCs) from 10X Genomics.
sce <- importExampleData("pbmc3k")
#> snapshotDate(): 2022-04-26
#> see ?TENxPBMCData and browseVignettes('TENxPBMCData') for documentation
#> Warning: Corrupt Cache: resource path
#> See AnnotationHub's TroubleshootingTheCache vignette section on corrupt cache
#> cache: C:\Users\Yichen\AppData\Local/R/cache/R/ExperimentHub
#> potential duplicate files:
#> 66c41363c8_1605
#> b1581a4f3a4c_1605
#> 66cb6b3970_1606
#> b15821a933a6_1606
#> 66c4fe3642_1607
#> b158265122b6_1607
#> 28582f9d3cbf_3508
#> 5e4c7beb372e_3508
#> 285859427542_3509
#> 5e4c531d2b58_3509
#> Continuing with first found cached file
#> downloading 1 resources
#> retrieving 1 resource
#> loading from cache
#> Warning: Corrupt Cache: resource path
#> See AnnotationHub's TroubleshootingTheCache vignette section on corrupt cache
#> cache: C:\Users\Yichen\AppData\Local/R/cache/R/ExperimentHub
#> potential duplicate files:
#> 66c41363c8_1605
#> b1581a4f3a4c_1605
#> 66cb6b3970_1606
#> b15821a933a6_1606
#> 66c4fe3642_1607
#> b158265122b6_1607
#> 28582f9d3cbf_3508
#> 5e4c7beb372e_3508
#> 285859427542_3509
#> 5e4c531d2b58_3509
#> Continuing with first found cached file
#> Warning: Corrupt Cache: resource path
#> See AnnotationHub's TroubleshootingTheCache vignette section on corrupt cache
#> cache: C:\Users\Yichen\AppData\Local/R/cache/R/ExperimentHub
#> potential duplicate files:
#> 66c41363c8_1605
#> b1581a4f3a4c_1605
#> 66cb6b3970_1606
#> b15821a933a6_1606
#> 66c4fe3642_1607
#> b158265122b6_1607
#> 28582f9d3cbf_3508
#> 5e4c7beb372e_3508
#> 285859427542_3509
#> 5e4c531d2b58_3509
#> Continuing with first found cached file
#> Warning: Corrupt Cache: resource path
#> See AnnotationHub's TroubleshootingTheCache vignette section on corrupt cache
#> cache: C:\Users\Yichen\AppData\Local/R/cache/R/ExperimentHub
#> potential duplicate files:
#> 66c41363c8_1605
#> b1581a4f3a4c_1605
#> 66cb6b3970_1606
#> b15821a933a6_1606
#> 66c4fe3642_1607
#> b158265122b6_1607
#> 28582f9d3cbf_3508
#> 5e4c7beb372e_3508
#> 285859427542_3509
#> 5e4c531d2b58_3509
#> Continuing with first found cached file
#> Warning: Corrupt Cache: resource path
#> See AnnotationHub's TroubleshootingTheCache vignette section on corrupt cache
#> cache: C:\Users\Yichen\AppData\Local/R/cache/R/ExperimentHub
#> potential duplicate files:
#> 66c41363c8_1605
#> b1581a4f3a4c_1605
#> 66cb6b3970_1606
#> b15821a933a6_1606
#> 66c4fe3642_1607
#> b158265122b6_1607
#> 28582f9d3cbf_3508
#> 5e4c7beb372e_3508
#> 285859427542_3509
#> 5e4c531d2b58_3509
#> Continuing with first found cached file
#> Warning: Corrupt Cache: resource path
#> See AnnotationHub's TroubleshootingTheCache vignette section on corrupt cache
#> cache: C:\Users\Yichen\AppData\Local/R/cache/R/ExperimentHub
#> potential duplicate files:
#> 66c41363c8_1605
#> b1581a4f3a4c_1605
#> 66cb6b3970_1606
#> b15821a933a6_1606
#> 66c4fe3642_1607
#> b158265122b6_1607
#> 28582f9d3cbf_3508
#> 5e4c7beb372e_3508
#> 285859427542_3509
#> 5e4c531d2b58_3509
#> Continuing with first found cached file