stitchRegions {dowser}

stitchRegions Similar to stitchVDJ but with segment IDs instead of nulecotides

Description

stitchRegions Similar to stitchVDJ but with segment IDs instead of nulecotides

Usage

stitchRegions(
  receptor,
  v_seq,
  d_seq,
  j_seq,
  np1_length = "np1_length",
  np2_length = "np1_length",
  n1_length = "n1_length",
  p3v_length = "p3v_length",
  p5d_length = "p5d_length",
  p3d_length = "p3d_length",
  n2_length = "n2_length",
  p5j_length = "p5j_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)

n1_length

Column name in receptor specifying n1 segment length (experimental)

p3v_length

Column name in receptor specifying p3v segment length (experimental)

p5d_length

Column name in receptor specifying p5d segment length (experimental)

p3d_length

Column name in receptor specifying p3d segment length (experimental)

n2_length

Column name in receptor specifying n2 segment length (experimental)

p5j_length

Column name in receptor specifying p5j segment length (experimental)

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 with segment IDs instead of nucleotides.

See Also

stitchVDJ