HeOrganAtlasData: Obtain the He organ atlas data

In LTLA/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

Obtain the He organ atlas data

Description

Obtain the human cortex single-nuclei RNA-seq data from Hu et al. (2017).

Usage

HeOrganAtlasData(
  tissue = c("Bladder", "Blood", "Common.bile.duct", "Esophagus", "Heart", "Liver",
    "Lymph.node", "Marrow", "Muscle", "Rectum", "Skin", "Small.intestine", "Spleen",
    "Stomach", "Trachea"),
  ensembl = FALSE,
  location = TRUE,
  legacy = FALSE
)

Arguments

tissue	Character vector specifying the tissues to return.
ensembl	Logical scalar indicating whether the output row names should contain Ensembl identifiers.
location	Logical scalar indicating whether genomic coordinates should be returned.
legacy	Logical scalar indicating whether to pull data from ExperimentHub. By default, we use data from the gypsum backend.

Details

Column data contains the tissue of origin, a variety of per-cell QC metrics well as some cell type annotations. The reclustered annotations required some assembly:

• reclustered.broad was generated based on whether the barcode was present in each *_meta.data.txt file at https://github.com/bei-lab/scRNA-AHCA.

• For each barcode that was present in one of those files, reclustered.fine was generated based on the label in the annotation field inside that file.

If multiple tissues are requested, counts are only reported for the intersection of genes across all tissues. This is because the gene annotation in the original count matrices differs across tissues.

If ensembl=TRUE, the gene symbols are converted to Ensembl IDs in the row names of the output object. Rows with missing Ensembl IDs are discarded, and only the first occurrence of duplicated IDs is retained.

If location=TRUE, the coordinates of the Ensembl gene models are stored in the rowRanges of the output. Note that this is only performed if ensembl=TRUE.

All data are downloaded from ExperimentHub and cached for local re-use. Specific resources can be retrieved by searching for scRNAseq/he-organ-atlas.

Value

A SingleCellExperiment object with a single matrix of UMI counts.

Author(s)

Aaron Lun

References

He S et al. (2020). Single-cell transcriptome profiling of an adult human cell atlas of 15 major organs. Genome Biol 21, 1:294.

Examples

if (.Machine$sizeof.pointer > 4) { # too large for 32-bit machines!
    sce <- HeOrganAtlasData()
}

LTLA/scRNAseq documentation built on June 28, 2024, 7:31 p.m.