View source: R/HumanPrimaryCellAtlasData.R
HumanPrimaryCellAtlasData | R Documentation |
Download and cache the normalized expression values of the data stored in the Human Primary Cell Atlas. The data will be downloaded from ExperimentHub, returning a SummarizedExperiment object for further use.
HumanPrimaryCellAtlasData(
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 for 713 microarray samples from the Human Primary Cell Atlas (HPCA) (Mabbott et al., 2013). These 713 samples were processed and normalized as described in Aran, Looney and Liu et al. (2019).
Each sample has been assigned to one of 37 main cell types ("label.main"
)
and 157 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
Mabbott NA et al. (2013). An expression atlas of human primary cells: inference of gene function from coexpression networks. BMC Genomics 14, Article 632.
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 <- HumanPrimaryCellAtlasData()
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