Example B cell single-cell RNA-seq data with pseudotime — example_sce

A SingleCellExperiment object containing a subset of B cells from the OneK1K cohort with associated individual metadata and a pseudotime trajectory. This dataset is useful for illustrating dynamic eQTL modeling along a continuous trajectory.

Usage

data("example_sce_Bcell")

Format

A SingleCellExperiment object with 817 genes and 3,726 cells.

assays

counts: raw UMI count matrix.
norm: normalized expression values.
logcounts: log-transformed normalized expression values.

rowData

A DataFrame with 2 columns:

GeneSymbol: Gene symbol.
features: Feature identifier (e.g., Ensembl ID).

colData

A DataFrame with 5 columns:

cell_type: Cell-type annotation within the B-cell compartment (e.g., immature/naive B cells, memory B cells).
indiv: Individual identifier.
sex: Sex of the donor.
age: Age of the donor.
slingPseudotime_1: Inferred pseudotime along a trajectory (e.g., from immature to memory B cells).

reducedDimNames

"PHATE": PHATE embedding used for trajectory inference and visualization.

Examples

data("example_sce_Bcell")
example_sce_Bcell
#> class: SingleCellExperiment 
#> dim: 817 3726 
#> metadata(0):
#> assays(3): counts norm logcounts
#> rownames(817): ENSG00000023902 ENSG00000028137 ... ENSG00000254709
#>   ENSG00000273272
#> rowData names(2): GeneSymbol features
#> colnames(3726): AAAGATGGTTATGCGT-1 AACTCAGGTCCGCTGA-1 ...
#>   TTCGAAGGTGATGCCC-9 TTGCCGTGTTCGTCTC-9
#> colData names(5): cell_type indiv sex age slingPseudotime_1
#> reducedDimNames(1): PHATE
#> mainExpName: NULL
#> altExpNames(0):
summary(SingleCellExperiment::colData(example_sce_Bcell)$slingPseudotime_1)
#>      Min.   1st Qu.    Median      Mean   3rd Qu.      Max. 
#> 0.0006717 0.2882431 0.4254734 0.4389588 0.5794676 0.9997564