DatabaseImmuneCellExpressionData {SingleR} | R Documentation

## 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")
    )

### 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

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()

[Package SingleR version 1.1.13 Index]