HumanPrimaryCellAtlasData: Obtain the HPCA data

In LTLA/celldex: Index of Reference Cell Type Datasets

Obtain the HPCA data

Description

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.

Usage

HumanPrimaryCellAtlasData(
  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 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.

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

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.

Examples

ref.se <- HumanPrimaryCellAtlasData()

LTLA/celldex documentation built on April 29, 2024, 4:34 p.m.