MonacoImmuneData {SingleR}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"))

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

The dataset contains 114 human RNA-seq samples annotated to 10 main cell types ("label.main"):

Samples were additionally annotated to 29 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

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()


[Package SingleR version 1.2.4 Index]