ImmGenData: Obtain mouse bulk expression data from the Immunologic Genome...
In LTLA/CellTypeReferences: Index of Reference Cell Type Datasets

ImmGenData

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"),
  legacy = 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.
`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.
`legacy`	Logical scalar indicating whether to pull data from ExperimentHub. By default, we use data from the gypsum backend.

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.