stitchVDJ: stitchVDJ combines germline gene segments to a single string

In dowser: B Cell Receptor Phylogenetics Toolkit

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.

dowser documentation built on May 29, 2024, 3:06 a.m.