expression2List {scRepertoire}R Documentation

Allows users to take the meta data in seurat/SCE and place it into a list that will work with all the functions

Description

Allows users to perform more fundamental measures of clonotype analysis using the meta data from the seurat or SCE object. For Seurat objects the active identity is automatically added as "cluster". Reamining grouping parameters or SCE or Seurat objects must appear in the meta data.

Usage

expression2List(sc, group)

Arguments

sc

object after combineExpression().

group

The column header to group the new list by

Value

list derived from the meta data of single-cell object with elements divided by the group parameter

Examples

#Getting the combined contigs
combined <- combineTCR(contig_list, rep(c("PX", "PY", "PZ"), each=2), 
rep(c("P", "T"), 3), cells ="T-AB")

#Getting a sample of a Seurat object
screp_example <- get(data("screp_example"))
sce <- suppressMessages(Seurat::UpdateSeuratObject(screp_example))
sce <- Seurat::as.SingleCellExperiment(sce)

#Using expression2List
newList <- expression2List(sce, group = "seurat_clusters")


[Package scRepertoire version 1.4.0 Index]