View source: R/MouseDropletData.R
MouseDropletData | R Documentation |
Obtain the processed counts for the mouse ageing thymus droplet scRNA-seq data set.
MouseDropletData(samples = NULL)
samples |
Integer or character vector specifying the samples for which data should be obtained.
If |
This function downloads the data for the mouse ageing thymus droplet scRNA-seq data from Baran-Gale et al. (2020).
The dataset contains 6 10X Genomics samples. The available samples are:
ZsG_1stRun1, ZsG_1stRun2, ZsG_2ndRun1, ZsG_2ndRun2, ZsG_3rdRun1, ZsG_3rdRun2
.
In the data, cell-containing libraries have already been identified in each sample
using the emptyDrops
function from DropletUtils.
The count matrix contains the raw count vectors for the cells called from all samples in this manner.
Size factors were computed using the computeSumFactors
function from scran.
The column metadata for called cells contains:
CellID
:Character, unique cell identifier across all samples.
SampID
:Character, Short unique identified for the experimental sample.
Class
:Character, Either Singlet or Multiplet Identifies cells called as a multiplet from hash-tag demultiplexing.
HTO
:Character, Hashtag oligo (HTO) character identifier, used for multiplexing experimental samples.
Age
:Character, Age of mouse at the time of doxycycline treatment. Age at time of data acquisition is +4weeks.
SortType
:Character, Flow cytometry sorting group, either ZsGreen+ (ZsGp) or ZsGreen- (ZsGn).
Cluster
:Integer, Cluster to which cells were assigned based on using the Walktrap community detection algorithm on a k-NN graph.
ClusterAnnot
:Character, Annotation assigned to cluster.
SizeFactor
:Numeric, Estimated normalized factor across all cells and experimental samples.
Reduced dimension representations of the data are also available in the reducedDims
slot of the SingleCellExperiment object.
The SingleCellExperiment
object has row metadata that contains the Ensembl ID ensembl_gene_id
and Gene
symbols external_gene_name
for each gene, as well as gene chromosome, strand and both start and end positions.
A SingleCellExperiment is returned containing processed data from selected samples.
List elements are named after the corresponding sample.
Mike Morgan, based on original code by Aaron Lun & Jonathan Griffiths
Mike Morgan
Baran-Gale J, Morgan MD, et al. (2020) Ageing compromises mouse thymus function and remodels epithelial cell differentiation eLife 9:e56221.
drop.data <- MouseDropletData(samples = "ZsG_1stRun1") drop.data
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