expression2List: Allows users to take the meta data in seurat/SCE and place it...

In scRepertoire: A toolkit for single-cell immune receptor profiling

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")

scRepertoire documentation built on Nov. 8, 2020, 7 p.m.