stitchVDJ - stitchVDJ combines germline gene segments to a single string

Description¶

stitchVDJ combines germline gene segments to a single string

Usage¶

stitchVDJ(
receptor,
v_seq,
d_seq,
j_seq,
np1_length = "np1_length",
np2_length = "np2_length",
np1_aa_length = "np1_aa_length",
np2_aa_length = "np2_aa_length",
amino_acid = FALSE
)

Arguments¶

receptor

row from AIRR-table containing sequence of interest

v_seq

germline V segment sequence from getGermline

d_seq

germline D segment sequence from getGermline

j_seq

germline J segment sequence from getGermline

np1_length

Column name in receptor specifying np1 segment length (e.g. np1_length)

np2_length

Column name in receptor specifying np2 segment length (e.g. np1_length)

np1_aa_length

Column name in receptor specifying np1 segment length in AA (if amino_acid=TRUE, e.g. np1_length)

np2_aa_length

Column name in receptor specifying np2 segment length in AA (if amino_acid=TRUE, e.g. np1_length)

amino_acid

Perform reconstruction on amino acid sequence (experimental)

Value¶

Full length germline VDJ sequence aligned with aligned with the sequence in the seq column of receptor.