buildClonalGermline - 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

Value¶

Tibble with reconstructed germlines

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

See also¶

createGermlines buildGermline, stitchVDJ