stitchVDJ {dowser}

stitchVDJ combines germline gene segments to a single string

Description

stitchVDJ combines germline gene segments to a single string

Usage

stitchVDJ(
  receptor,
  v_seq,
  d_seq,
  j_seq,
  np1_length = "np1_length",
  np2_length = "np2_length",
  np1_aa_length = "np1_aa_length",
  np2_aa_length = "np2_aa_length",
  amino_acid = FALSE
)

Arguments

receptor

row from AIRR-table containing sequence of interest

v_seq

germline V segment sequence from getGermline

d_seq

germline D segment sequence from getGermline

j_seq

germline J segment sequence from getGermline

np1_length

Column name in receptor specifying np1 segment length (e.g. np1_length)

np2_length

Column name in receptor specifying np2 segment length (e.g. np1_length)

np1_aa_length

Column name in receptor specifying np1 segment length in AA (if amino_acid=TRUE, e.g. np1_length)

np2_aa_length

Column name in receptor specifying np2 segment length in AA (if amino_acid=TRUE, e.g. np1_length)

amino_acid

Perform reconstruction on amino acid sequence (experimental)

Value

Full length germline VDJ sequence aligned with aligned with the sequence in the seq column of receptor.