combineExpression: Adding clonotype information to a seurat or SCE object

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

Description

This function adds the immune receptor information to the seurat or SCE object to the meta data. By defualt this function also calculates the frequencies of the clonotypes by sequencing run (groupBy = "none"). To change how the frequencies are calculated, select a column header for the groupBy variable. Importantly, before using combineExpression() ensure the barcodes of the seurat or SCE object match the barcodes in the output of the combinedContig() call. Check changeNames() to change the prefix of the seurat object. If the dominant clonotypes have a greater frequency than 500, adjust the cloneTypes variable.

Usage

combineExpression(
  df,
  sc,
  cloneCall = "gene+nt",
  groupBy = "none",
  cloneTypes = c(None = 0, Single = 1, Small = 5, Medium = 20, Large = 100,
    Hyperexpanded = 500),
  filterNA = FALSE
)

Arguments

df	The product of CombineTCR() or CombineBCR().
sc	The seurat or SingleCellExperiment (SCE) object to attach
cloneCall	How to call the clonotype - CDR3 gene (gene), CDR3 nucleotide (nt) CDR3 amino acid (aa), or CDR3 gene+nucleotide (gene+nt).
groupBy	The column label in the combined contig object in which clonotype frequency will be calculated.
cloneTypes	The bins for the grouping based on frequency
filterNA	Method to subset seurat object of barcodes without clonotype information

Value

seurat or SingleCellExperiment object with attached clonotype information

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 combineExpresion()
sce <- combineExpression(combined, sce)

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