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_id = "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_id
- 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¶
- 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.