buildClonalGermline {dowser}

buildClonalGermline Determine consensus clone sequence and create germline for clone

Description

Determine consensus clone sequence and create germline for clone

Usage

buildClonalGermline(
  receptors,
  references,
  chain = "IGH",
  use_regions = FALSE,
  vonly = FALSE,
  seq = "sequence_alignment",
  id = "sequence_id",
  clone = "clone_id",
  v_call = "v_call",
  j_call = "j_call",
  j_germ_length = "j_germline_length",
  j_germ_aa_length = "j_germline_aa_length",
  amino_acid = FALSE,
  ...
)

Arguments

receptors

AIRR-table containing sequences from one clone

references

Full list of reference segments, see readIMGT

chain

chain in references being analyzed

use_regions

Return string of VDJ regions? (optional)

vonly

Return germline of only v segment?

seq

Column name for sequence alignment

id

Column name for sequence ID

clone

Column name for clone ID

v_call

Column name for V gene segment gene call

j_call

Column name for J gene segment gene call

j_germ_length

Column name of J segment length within germline

j_germ_aa_length

Column name of J segment amino acid length (if amino_acid=TRUE)

amino_acid

Perform reconstruction on amino acid sequence (experimental)

...

Additional arguments passed to buildGermline

Details

Return object adds/edits following columns:

• seq: Sequences potentially padded same length as germline

• germline_alignment: Full length germline

• germline_alignment_d_mask: Full length, D region masked

• vonly: V gene segment of germline if vonly=TRUE

• regions: String of VDJ segment in position if use_regions=TRUE

Value

Tibble with reconstructed germlines

See Also

createGermlines buildGermline, stitchVDJ