BlueprintEncodeData {SingleR} | R Documentation

## Obtain human bulk RNA-seq data from Blueprint and ENCODE

### Description

Download and cache the normalized expression values of 259 RNA-seq samples of pure stroma and immune cells as generated and supplied by Blueprint and ENCODE.

### Usage

    BlueprintEncodeData(
      rm.NA = c("rows", "cols", "both", "none"),
      ensembl = FALSE,
      cell.ont = c("all", "nonna", "none")
    )

### Arguments

`rm.NA` | String specifying how missing values should be handled. `"rows"` will remove genes with at least one missing value, `"cols"` will remove samples with at least one missing value, `"both"` will remove any gene or sample with at least one missing value, and `"none"` will not perform any removal.
`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.

### Details

This function provides normalized expression values for 259 bulk RNA-seq samples generated by Blueprint and ENCODE from pure populations of stroma and immune cells (Martens and Stunnenberg, 2013; The ENCODE Consortium, 2012). The samples were processed and normalized as described in Aran, Looney and Liu et al. (2019), i.e., the raw RNA-seq counts were downloaded from Blueprint and ENCODE in 2016 and normalized via edgeR (TPMs).

Blueprint Epigenomics contains 144 RNA-seq pure immune samples annotated to 28 cell types. ENCODE contains 115 RNA-seq pure stroma and immune samples annotated to 17 cell types. All together, this reference contains 259 samples with 43 cell types (`"label.fine"`), manually aggregated into 24 broad classes (`"label.main"`). The fine labels 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

The ENCODE Project Consortium (2012). An integrated encyclopedia of DNA elements in the human genome. Nature 489, pages 57–74.

Martens JHA and Stunnenberg HG (2013). BLUEPRINT: mapping human blood cell epigenomes. Haematologica 98, 1487–1489.

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 <- BlueprintEncodeData(rm.NA = "rows")

[Package SingleR version 1.1.13 Index]