getSubclones - Define subclones based on light chain rearrangements

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

Details

  1. Make temporary array containing light chain clones
  2. Enumerate all possible V and J combinations
  3. Determine which combination is the most frequent
  4. Assign sequences with that combination to clone t
  5. Copy those sequences to return array
  6. Remove all cells with that combination from temp array
  7. Repeat 1-5 until temporary array zero. If there is more than rearrangement with the same V/J in the same cell, pick the one with the highest non-ambiguous characters.