ImmGenData | R Documentation |
Download and cache the normalized expression values of 830 microarray samples of pure mouse immune cells, generated by the Immunologic Genome Project (ImmGen).
ImmGenData(
ensembl = FALSE,
cell.ont = c("all", "nonna", "none"),
legacy = FALSE
)
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 |
legacy |
Logical scalar indicating whether to pull data from ExperimentHub. By default, we use data from the gypsum backend. |
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.
A SummarizedExperiment object with a "logcounts"
assay
containing the log-normalized expression values, along with cell type labels in the
colData
.
Friederike Dündar
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.
ref.se <- ImmGenData()
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