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"`):

- Basophils

- B cells

- CMPs

- Dendritic cells

- Eosinophils

- Erythroid cells

- GMPS

- Granulocytes

- HSCs

- Megakaryocytes

- MEPs

- Monocytes

- NK cells

- NK T cells

- CD8+ T cells

- CD4+ T cells

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

- Basophils

- Naive B cells

- Mature B cells class able to switch

- Mature B cells

- Mature B cells class switched

- Common myeloid progenitors

- Plasmacytoid Dendritic Cells

- Myeloid Dendritic Cells

- Eosinophils

- Erythroid_CD34+ CD71+ GlyA-

- Erythroid_CD34- CD71+ GlyA-

- Erythroid_CD34- CD71+ GlyA+

- Erythroid_CD34- CD71lo GlyA+

- Erythroid_CD34- CD71- GlyA+

- Granulocyte/monocyte progenitors

- Colony Forming Unit-Granulocytes

- Granulocyte (Neutrophilic Metamyelocytes)

- Granulocyte (Neutrophils)

- Hematopoietic stem cells_CD133+ CD34dim

- Hematopoietic stem cell_CD38- CD34+

- Colony Forming Unit-Megakaryocytic

- Megakaryocytes

- Megakaryocyte/erythroid progenitors

- Colony Forming Unit-Monocytes

- Monocytes

- Mature NK cells_CD56- CD16+ CD3-

- Mature NK cells_CD56+ CD16+ CD3-

- Mature NK cells_CD56- CD16- CD3-

- NK T cells

- Early B cells

- Pro B cells

- CD8+ Effector Memory RA

- Naive CD8+ T cells

- CD8+ Effector Memory

- CD8+ Central Memory

- Naive CD4+ T cells

- CD4+ Effector Memory

- CD4+ Central Memory

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 1.1.13 Index]