getGermline {dowser}

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.