getGermline: getGermline get germline segment from specified receptor and...

In dowser: B Cell Receptor Phylogenetics Toolkit

getGermline get germline segment from specified receptor and segment

Description

getGermline get germline segment from specified receptor and segment

Usage

getGermline(
  receptor,
  references,
  segment,
  field,
  germ_start,
  germ_end,
  germ_length,
  germ_aa_start,
  germ_aa_length,
  amino_acid = FALSE
)

Arguments

receptor	row from AIRR-table containing sequence of interest
references	list of reference segments. Must be specific to locus and segment
segment	Gene segment to search. Must be V, D, or J.
field	Column name for segment gene call (e.g. v_call)
germ_start	Column name of index of segment start within germline segment (e.g. v_germline_start)
germ_end	Similar to germ_start, but specifies end of segment (e.g. v_germline_end)
germ_length	Similar to germ_start, but specifies length of segment (e.g. v_germline_end)
germ_aa_start	Column name of index of segment start within germline segment in AA (if amino_acid=TRUE, e.g. v_germline_start)
germ_aa_length	Similar to germ_start, but specifies length of segment in AA (if amino_acid=TRUE, e.g. v_germline_end)
amino_acid	Perform reconstruction on amino acid sequence (experimental)

Value

String of germline sequence from specified segment aligned with the sequence in the seq column of receptor.

dowser documentation built on Nov. 5, 2025, 6:36 p.m.