buildGermline - 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)

Value¶

List of reconstructed germlines

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

See also¶

buildClonalGermline, stitchVDJ