HumanPrimaryCellAtlasData {SingleR} | R Documentation

## 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)

### 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.

### Details

This function provides normalized expression values 713 microarray samples of 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) and each sample has been assigned to one of 37 main cell types and 157 subtypes.

### 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()

[Package SingleR version 1.0.6 Index]