View source: R/DatabaseImmuneExpressionData.R
DatabaseImmuneCellExpressionData | R Documentation |
Download and cache the normalized expression values of 1561 bulk RNA-seq samples of sorted cell populations from the Database of Immune Cell Expression (DICE).
DatabaseImmuneCellExpressionData(
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 1561 bulk RNA-seq samples generated by DICE from pure populations of human immune cells.
TPM normalized values for each cell type were downloaded from https://dice-database.org/downloads. Genes with no reads across samples were removed, and values were log2 normalized after a pseudocount of 1 was added.
The dataset contains 1561 human RNA-seq samples annotated to 5 main cell types ("label.main"
):
B cells
Monocytes
NK cells
T cells, CD8+
T cells, CD4+
Samples were additionally annotated to 15 fine cell types ("label.fine"
):
B cells, naive
Monocytes, CD14+
Monocytes, CD16+
NK cells
T cells, memory TREG
T cells, CD4+, naive
T cells, CD4+, naive, stimulated
T cells, CD4+, naive Treg
T cells, CD4+, Th1
T cells, CD4+, Th1_17
T cells, CD4+, Th2
T cells, CD8+, naïve
T cells, CD8+, naïve, stimulated
T cells, CD4+, TFH
T cells, CD4+, Th17
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
.
Jared Andrews
Schmiedel B et al. (2018). Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression. Cell 175, 1701-1715.
ref.se <- DatabaseImmuneCellExpressionData()
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