DatabaseImmuneCellExpressionData: Obtain human bulk RNA-seq data from DICE

In LTLA/celldex: Index of Reference Cell Type Datasets

Obtain human bulk RNA-seq data from DICE

Description

Download and cache the normalized expression values of 1561 bulk RNA-seq samples of sorted cell populations from the Database of Immune Cell Expression (DICE).

Usage

DatabaseImmuneCellExpressionData(
  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

This function provides normalized expression values of 1561 bulk RNA-seq samples generated by DICE from pure populations of human immune cells.

TPM normalized values for each cell type were downloaded from https://dice-database.org/downloads. Genes with no reads across samples were removed, and values were log2 normalized after a pseudocount of 1 was added.

The dataset contains 1561 human RNA-seq samples annotated to 5 main cell types ("label.main"):

• B cells

• Monocytes

• NK cells

• T cells, CD8+

• T cells, CD4+

Samples were additionally annotated to 15 fine cell types ("label.fine"):

• B cells, naive

• Monocytes, CD14+

• Monocytes, CD16+

• NK cells

• T cells, memory TREG

• T cells, CD4+, naive

• T cells, CD4+, naive, stimulated

• T cells, CD4+, naive Treg

• T cells, CD4+, Th1

• T cells, CD4+, Th1_17

• T cells, CD4+, Th2

• T cells, CD8+, naïve

• T cells, CD8+, naïve, stimulated

• T cells, CD4+, TFH

• T cells, CD4+, Th17

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

Schmiedel B et al. (2018). Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression. Cell 175, 1701-1715.

Examples

ref.se <- DatabaseImmuneCellExpressionData()

LTLA/celldex documentation built on March 19, 2024, 6:33 p.m.