getSubclones {dowser}

#' Deprecated! Use resolveLightChains

Description

getSubClones plots a tree or group of trees

Usage

getSubclones(
  heavy,
  light,
  nproc = 1,
  minseq = 1,
  id = "sequence_id",
  seq = "sequence_alignment",
  clone = "clone_id",
  cell = "cell_id",
  v_call = "v_call",
  j_call = "j_call",
  junc_len = "junction_length",
  nolight = "missing"
)

Arguments

heavy

a tibble containing heavy chain sequences with clone_id

light

a tibble containing light chain sequences

nproc

number of cores for parallelization

minseq

minimum number of sequences per clone

id

name of the column containing sequence identifiers.

seq

name of the column containing observed DNA sequences. All sequences in this column must be multiple aligned.

clone

name of the column containing the identifier for the clone. All entries in this column should be identical.

cell

name of the column containing identifier for cells.

v_call

name of the column containing V-segment allele assignments. All entries in this column should be identical to the gene level.

j_call

name of the column containing J-segment allele assignments. All entries in this column should be identical to the gene level.

junc_len

name of the column containing the length of the junction as a numeric value. All entries in this column should be identical for any given clone.

nolight

string to use to indicate a missing light chain

Value

a tibble containing