getSubclones - Define subclones based on light chain rearrangements
getSubclones plots a tree or group of trees
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" )
- a tibble containing heavy chain sequences with clone_id
- a tibble containing light chain sequences
- number of cores for parallelization
- minimum number of sequences per clone
- name of the column containing sequence identifiers.
- name of the column containing observed DNA sequences. All sequences in this column must be multiple aligned.
- name of the column containing the identifier for the clone. All entries in this column should be identical.
- name of the column containing identifier for cells.
- name of the column containing V-segment allele assignments. All entries in this column should be identical to the gene level.
- name of the column containing J-segment allele assignments. All entries in this column should be identical to the gene level.
- 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.
- string to use to indicate a missing light chain
a tibble containing
- Make temporary array containing light chain clones
- Enumerate all possible V and J combinations
- Determine which combination is the most frequent
- Assign sequences with that combination to clone t
- Copy those sequences to return array
- Remove all cells with that combination from temp array
- 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.