ImmGenData {SingleR} | R Documentation

## Obtain mouse bulk expression data from the Immunologic Genome Project

### Description

Download and cache the normalized expression values of 830 microarray samples of pure mouse immune cells, generated by the Immunologic Genome Project (ImmGen).

### Usage

    ImmGenData(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 830 microarray samples generated by ImmGen from pure populations of murine immune cells (<http://www.immgen.org/>). The samples were processed and normalized as described in Aran, Looney and Liu et al. (2019), i.e., CEL files from the Gene Expression Omnibus (GEO; GSE15907 and GSE37448), were downloaded, processed, and normalized using the robust multi-array average (RMA) procedure on probe-level data.

This dataset consists of 20 broad cell types (`"label.main"`) and 253 finely resolved cell subtypes (`"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)

Friederike Dündar

### References

Heng TS, Painter MW, Immunological Genome Project Consortium (2008). The Immunological Genome Project: networks of gene expression in immune cells. Nat. Immunol. 9, 1091-1094.

Aran D, Looney AP, Liu L et al. (2019). Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat. Immunol. 20, 163–172.

### Examples

    ref.se <- ImmGenData()

[Package SingleR version 1.1.13 Index]