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"):

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

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 1.2.4 Index]