MonacoImmuneData: Obtain bulk RNA-seq data of sorted human immune cells
In LTLA/CellTypeReferences: Index of Reference Cell Type Datasets

MonacoImmuneData

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"),
  legacy = FALSE
)

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.
`legacy`	Logical scalar indicating whether to pull data from ExperimentHub. By default, we use data from the gypsum backend.

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.