MonacoImmuneData: Obtain bulk RNA-seq data of sorted human immune cells

View source: R/MonacoImmuneData.R

MonacoImmuneDataR 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.

Examples

ref.se <- MonacoImmuneData()


LTLA/celldex documentation built on June 3, 2024, 4:53 p.m.