MonacoImmuneData {SingleR} | R Documentation

## Obtain bulk RNA-seq data of sorted human immune cells

### Description

Download and cache the normalized expression values of 114 bulk RNA-seq samples of sorted immune cell populations that can be found in GSE107011.

### Usage

    MonacoImmuneData(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 114 human RNA-seq samples annotated to 10 main cell types (`"label.main"`):

- CD8+ T cells

- T cells

- CD4+ T cells

- Progenitors

- B cells

- Monocytes

- NK cells

- Dendritic cells

- Neutrophils

- Basophils

Samples were additionally annotated to 29 fine cell types (`"label.fine"`):

- Naive CD8 T cells

- Central memory CD8 T cells

- Effector memory CD8 T cells

- Terminal effector CD8 T cells

- MAIT cells

- Vd2 gd T cells

- Non-Vd2 gd T cells

- Follicular helper T cells

- T regulatory cells

- Th1 cells

- Th1/Th17 cells

- Th17 cells

- Th2 cells

- Naive CD4 T cells

- Terminal effector CD4 T cells

- Progenitor cells

- Naive B cells

- Non-switched memory B cells

- Exhausted B cells

- Switched memory B cells

- Plasmablasts

- Classical monocytes

- Intermediate monocytes

- Non classical monocytes

- Natural killer cells

- Plasmacytoid dendritic cells

- Myeloid dendritic cells

- Low-density neutrophils

- Low-density basophils

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

Monaco G et al. (2019). RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types Cell Rep. 26, 1627-1640.

### Examples

    ref.se <- MonacoImmuneData()

[Package SingleR version 1.1.13 Index]