select_clusters: Split the immune repertoire data to clusters from single-cell...

In immunomind/immunarch: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires

Split the immune repertoire data to clusters from single-cell barcodes

Description

Given the vector of barcodes from Seurat, splits the input repertoires to separate subsets following the barcodes' assigned IDs. Useful in case you want to split immune repertoires by patients or clusters.

Usage

select_clusters(.data, .clusters, .field = "Cluster")

Arguments

.data	List of two elements "data" and "meta", with "data" being a list of immune repertoires, and "meta" being a metadata table.
.clusters	Factor vector with barcodes as vector names and cluster IDs as vector elements. The output of the Seurat Idents function works.
.field	A string specifying the name of the field in the input metadata. New immune repertoire subsets will have cluster IDs in this field.

Value

A list with two elements "data" and "meta" with updated immune repertoire tables and metadata.

See Also

select_barcodes

Examples

## Not run: 
library(Seurat)
Idents(pbmc_small)
new_cluster_ids <- c("A", "B", "C")
new_cluster_ids <- levels(pbmc_small)
new_cluster_ids
pbmc_small <- RenameIdents(pbmc_small, new_cluster_ids)

## End(Not run)

immunomind/immunarch documentation built on March 20, 2024, 12:01 p.m.