| getSubclones {dowser} | R Documentation |
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"
)
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 |
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.
a tibble containing