groupGenes - Group sequences by gene assignment
groupGenes will group rows by shared V and J gene assignments.
In the case of ambiguous (multiple) gene assignments, the grouping will
be a union across all ambiguous V and J gene pairs, analagous to
single-linkage clustering (i.e., allowing for chaining).
groupGenes(data, v_call = "V_CALL", j_call = "J_CALL", first = FALSE)
- data.frame containing sequence data.
- name of the column containing the V-segment allele calls.
- name of the column containing the J-segment allele calls.
TRUEonly the first call of the gene assignments is used. if
FALSEthe union of ambiguous gene assignments is used to group all sequences with any overlapping gene calls.
Returns a modified
data data.frame with union indices
All rows containing
NA valies in their
j_call column will be removed.
A warning will be issued when a row containing an
NA is removed.
Ambiguous gene assignments are assumed to be separated by commas.
# Group by genes db <- groupGenes(ExampleDb)