buildAllClonalGermlines: buildAllClonalGermlines Determines and builds all possible...

In dowser: B Cell Receptor Phylogenetics Toolkit

buildAllClonalGermlines Determines and builds all possible germlines for a clone

Description

buildAllClonalGermlines Determines and builds all possible germlines for a clone

Usage

buildAllClonalGermlines(
  receptors,
  references,
  chain = "IGH",
  use_regions = FALSE,
  vonly = FALSE,
  seq = "sequence_alignment",
  id = "sequence_id",
  clone = "clone_id",
  v_call = "v_call",
  j_call = "j_call",
  v_germ_start = "v_germline_start",
  v_germ_end = "v_germline_end",
  v_germ_length = "v_germline_length",
  d_germ_start = "d_germline_start",
  d_germ_end = "d_germline_end",
  d_germ_length = "d_germline_length",
  j_germ_start = "j_germline_start",
  j_germ_end = "j_germline_end",
  j_germ_length = "j_germline_length",
  np1_length = "np1_length",
  np2_length = "np2_length",
  j_germ_aa_length = "j_germline_aa_length",
  amino_acid = FALSE,
  ...
)

Arguments

receptors	AIRR-table containing sequences from one clone
references	Full list of reference segments, see readIMGT
chain	chain in references being analyzed
use_regions	Return string of VDJ regions? (optional)
vonly	Return germline of only v segment?
seq	Column name for sequence alignment
id	Column name for sequence ID
clone	Column name for clone ID
v_call	Column name for V gene segment gene call
j_call	Column name for J gene segment gene call
v_germ_start	Column name of index of V segment start within germline
v_germ_end	Column name of index of V segment end within germline
v_germ_length	Column name of index of V segment length within germline
d_germ_start	Column name of index of D segment start within germline
d_germ_end	Column name of index of D segment end within germline
d_germ_length	Column name of index of D segment length within germline
j_germ_start	Column name of index of J segment start within germline
j_germ_end	Column name of index of J segment end within germline
j_germ_length	Column name of index of J segment length within germline
np1_length	Column name in receptor specifying np1 segment length
np2_length	Column name in receptor specifying np2 segment length
j_germ_aa_length	Column name of J segment amino acid length (if amino_acid=TRUE)
amino_acid	Perform reconstruction on amino acid sequence (experimental)
...	Additional arguments passed to buildGermline

Value

A data frame with all possible reconstructed germlines

See Also

createAllGermlines buildGermline, stitchVDJ

dowser documentation built on Aug. 20, 2026, 5:06 p.m.