NovershternHematopoieticData {SingleR}R Documentation

Obtain bulk microarray expression for sorted hematopoietic cells

Description

Download and cache the normalized expression values of 211 bulk human microarray samples of sorted hematopoietic cell populations that can be found in GSE24759.

Usage

NovershternHematopoieticData(
  ensembl = FALSE,
  cell.ont = c("all", "nonna", "none")
)

Arguments

ensembl

Logical scalar indicating whether to convert row names to Ensembl IDs. Genes without a mapping to a non-duplicated Ensembl ID are discarded.

cell.ont

String specifying whether Cell Ontology terms should be included in the colData. If "nonna", all samples without a valid term are discarded; if "all", all samples are returned with (possibly NA) terms; if "none", terms are not added.

Details

The dataset contains 211 human microarray samples annotated to 16 main cell types ("label.main"):

Samples were additionally annotated to 38 fine cell types ("label.fine"):

The subtypes have also been mapped to the Cell Ontology ("label.ont", if cell.ont is not "none"), which can be used for further programmatic queries.

Value

A SummarizedExperiment object with a "logcounts" assay containing the log-normalized expression values, along with cell type labels in the colData.

Author(s)

Jared Andrews

References

Novershtern N et al. (2011). Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 144, 296-309.

Examples

ref.se <- NovershternHematopoieticData()


[Package SingleR version 1.2.4 Index]