assign_clonotypes: Function to use for assigning clonotypes based on custom...

In keshav-motwani/scanalysis: Multi-Sample Visualization and Immune Repertoire Analysis Utilities for Single-Cell Data

Description

Function to use for assigning clonotypes based on custom definition

Usage

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

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keshav-motwani/scanalysis documentation built on Feb. 4, 2021, 2:21 a.m.