Skip to contents

Adding Clonal Information to Single-Cell Object

Source: R/combineExpression.R
combineExpression.Rd

This function adds the immune receptor information to the Seurat or SCE object to the meta data. By default this function also calculates the frequencies and proportion of the clones by sequencing run (group.by = NULL). To change how the frequencies/proportions are calculated, select a column header for the group.by variable. Importantly, before using combineExpression() ensure the barcodes of the single-cell object object match the barcodes in the output of the combineTCR() or combineBCR().

Usage

combineExpression(
  input.data,
  sc.data,
  clone.call = NULL,
  chain = "both",
  group.by = NULL,
  proportion = TRUE,
  filter.na = NULL,
  clone.size = NULL,
  add.label = NULL,
  cloneCall = NULL,
  cloneSize = NULL,
  filterNA = NULL,
  addLabel = NULL
)

Arguments

input.data

The product of combineTCR(), combineBCR() or a list of both c(combineTCR(), combineBCR()).

sc.data

The Seurat or Single-Cell Experiment (SCE) object to attach

clone.call

Defines the clonal sequence grouping. Accepted values are: gene (VDJC genes), nt (CDR3 nucleotide sequence), aa (CDR3 amino acid sequence), or strict (VDJC + nt). A custom column header can also be used.

chain

The TCR/BCR chain to use. Use both to include both chains (e.g., TRA/TRB). Accepted values: TRA, TRB, TRG, TRD, IGH, IGL (for both light chains), both.

group.by

A column header in lists to group the analysis by (e.g., "sample", "treatment"). If NULL, will be based on the list element.

proportion

Whether to proportion (TRUE) or total frequency (FALSE) of the clone based on the group.by variable.

filter.na

Method to subset Seurat/SCE object of barcodes without clone information

clone.size

The bins for the grouping based on proportion or frequency. If proportion is FALSE and the clone.sizes are not set high enough based on frequency, the upper limit of clone.sizes will be automatically updated.

add.label

This will add a label to the frequency header, allowing the user to try multiple group.by variables or recalculate frequencies after subsetting the data.

cloneCall

[Deprecated] Use clone.call instead.

cloneSize

[Deprecated] Use clone.size instead.

filterNA

[Deprecated] Use filter.na instead.

addLabel

[Deprecated] Use add.label instead.

Value

Single-cell object with clone information added to meta data information

Examples

# Getting the combined contigs
combined <- combineTCR(contig_list, 
                        samples = c("P17B", "P17L", "P18B", "P18L", 
                                    "P19B","P19L", "P20B", "P20L"))

# Getting a sample of a Seurat object
scRep_example <- get(data("scRep_example"))

# Using combineExpresion()
scRep_example <- combineExpression(combined, scRep_example)