CoNGAfy: Reduce a single-cell object to representative cells

In ncborcherding/Trex: Methods for TCR single-cell embedding

Reduce a single-cell object to representative cells

Description

Generate a single-cell object that has a representation of RNA expression by clonotype. This approach was first introduced in CoNGA and was adapted to R. Please read and cite the author's work.

Usage

CoNGAfy(
  input.data,
  method = "dist",
  features = NULL,
  assay = "RNA",
  meta.carry = c("CTaa", "CTgene")
)

Arguments

input.data	Single Cell Object in Seurat or Single Cell Experiment format
method	"mean" or "dist" Generate a mean value across features by clonotype or use the PCA reduction to identify the cell with the minimal euclidean distance from the clonotype group.
features	Selected genes for the reduction DEFAULT: null will return all genes
assay	The name of the assay or assays to return.
meta.carry	Variables to carry over from the meta data of the single-cell object

Value

Single-cell Object with one cell representing a single clone

Examples

trex_values <- CoNGAfy(trex_example, 
                       method = "dist",
                       features = NULL)
                        

ncborcherding/Trex documentation built on Nov. 4, 2024, 10:31 p.m.