buildGermline reconstruct germline segments from alignment dataReconstruct germlines from alignment data.
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
)List of reconstructed germlines
row from AIRR-table containing sequence of interest
list of reference segments. Must be specific to locus
Column name for sequence alignment
Column name for sequence ID
Column name for clone ID
Column name for V gene segment gene call
Column name for D gene segment gene call
Column name for J gene segment gene call
Column name of index of V segment start within germline
Column name of index of V segment end within germline
Column name of index of V segment length within germline
Column name of index of D segment start within germline
Column name of index of D segment end within germline
Column name of index of D segment length within germline
Column name of index of J segment start within germline
Column name of index of J segment end within germline
Column name of index of J segment length within germline
Column name in receptor specifying np1 segment length
Column name in receptor specifying np2 segment length
Perform reconstruction on amino acid sequence (experimental)
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
buildClonalGermline, stitchVDJ