treg-data {RPointCloud}

Single Cell Data on T Regulatory (Treg) Cells

Description

This data set contains mRNA and protein-antibody data on T-regulatory immune cells. It is a subset of a much larger data set collected from the peripheral blood of patients with a variety of health comnditions.

Usage

data(treg)

Format

Note that there are three distinct objects included in the data set: treg, tmat, and rip.

treg

A numerical data matrix with 538 rows and 255 columns. Each column represents a single cell from one of 61 samples that were assayed by (mixed-omics) single cell sequencing. Each row represents one of the features that was measured in the assay. Of these, 51 are antibodies that were tagged with an RNA barcode to identify them; their names all end with the string pAbO. The remaining 487 features are mRNA measurements, named by their official gene symbol at the time the experiment was performed. Each column represents a different single cell. This matrix is a subset of a more complete data set of T regulatory cells (Tregs). It was produced using the downsample function from the Mercator package, which was in turn inspired by a similar routine used in the SPADE algorithm by Peng Qiu. A key point of the algorithm is to make sampling less likely from the densest part of the distribution in order to preserve rare cell types in the population.

tmat

A distance matrix, stored as a dist object, produced using Pearson correlation as a measure of distance between sigle-cell vectors in the treg data set.

rip

This object is a "Rips diagram". It was produced by running the the ripsDiag function from the TDA R package on the treg subset of single cells.

Author(s)

Kevin R. Coombes [e-mail], Jake Reed [e-mail]

Source

Data were kindly provided by Dr. Klaus Ley, director of the Georgia Immunolgy Center at Augusta University. Analysis to perform cell typing with Seurat and isolate the subset of 769 T regulatory cells found in dset was performed by Jake Reed, as was the downsampling to select the random subset of 255 cells in the treg subset and use them for topolgical data analysis to compute the rip object.

References

Qiu P, Simonds EF, Bendall SC, Gibbs KD Jr, Bruggner RV, Linderman MD, Sachs K, Nolan GP, Plevritis SK. Extracting a cellular hierarchy from high-dimensional cytometry data with SPADE. Nat Biotechnol. 2011 Oct 2;29(10):886-91. doi: 10.1038/nbt.1991.