Function to use for assigning clonotypes based on custom definition

Source: R/assign_clonotypes.R

Function to use for assigning clonotypes based on custom definition

assign_clonotypes(
  sce,
  clonotype_fields = c("v_gene", "cdr3", "j_gene"),
  chains = c("TRA", "TRB"),
  tra_range = c(0, 2),
  trb_range = c(0, 1),
  igl_range = c(0, 2),
  igk_range = c(0, 2),
  igh_range = c(0, 1),
  name = "clonotype"
)

Arguments

sce

SingleCellExperiment object
clonotype_fields

fields to include in clonotype definition (e.g., c("v_gene", "cdr3", "j_gene", etc.))
chains

chains which to include in clonotype definition(e.g., c("TRA", "TRB"))
tra/trb/igl/igk/igh_range

vector of length 2 with minimum and maximum number of unique chains (inclusive)

Value

SingleCellExperiment object with added columns to colData including "clonotype", "clonotype_count", and "clonotype_count_2:10"

Examples

NULL
#> NULL