buildGermline: 'buildGermline' reconstruct germline segments from alignment...

In dowser: B Cell Receptor Phylogenetics Toolkit

buildGermline reconstruct germline segments from alignment data

Description

Reconstruct germlines from alignment data.

Usage

buildGermline(
  receptor,
  references,
  seq = "sequence_alignment",
  id = "sequence_id",
  clone = "clone_id",
  v_call = "v_call",
  d_call = "d_call",
  j_call = "j_call",
  v_germ_start = "v_germline_start",
  v_germ_end = "v_germline_end",
  v_germ_length = "v_germline_length",
  d_germ_start = "d_germline_start",
  d_germ_end = "d_germline_end",
  d_germ_length = "d_germline_length",
  j_germ_start = "j_germline_start",
  j_germ_end = "j_germline_end",
  j_germ_length = "j_germline_length",
  np1_length = "np1_length",
  np2_length = "np2_length",
  amino_acid = FALSE
)

Arguments

receptor	row from AIRR-table containing sequence of interest
references	list of reference segments. Must be specific to locus
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
d_call	Column name for D gene segment gene call
j_call	Column name for J gene segment gene call
v_germ_start	Column name of index of V segment start within germline
v_germ_end	Column name of index of V segment end within germline
v_germ_length	Column name of index of V segment length within germline
d_germ_start	Column name of index of D segment start within germline
d_germ_end	Column name of index of D segment end within germline
d_germ_length	Column name of index of D segment length within germline
j_germ_start	Column name of index of J segment start within germline
j_germ_end	Column name of index of J segment end within germline
j_germ_length	Column name of index of J segment length within germline
np1_length	Column name in receptor specifying np1 segment length
np2_length	Column name in receptor specifying np2 segment length
amino_acid	Perform reconstruction on amino acid sequence (experimental)

Details

Return object contains multiple IMGT-gapped germlines:

• full: Full length germline

• dmask: Full length germline with D region masked

• vonly: V gene segment of germline

• regions: String showing VDJ segment of each position

Value

List of reconstructed germlines

See Also

buildClonalGermline, stitchVDJ

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