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)

### 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.

### 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 (with Matlab functions).

The data will be downloaded from ExperimentHub, returning a SummarizedExperiment object for further use.

### 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 1.0.6 Index]