stitchRegions - stitchRegions Similar to stitchVDJ but with segment IDs instead of nucleotides
Description¶
stitchRegions Similar to stitchVDJ but with segment IDs instead of nucleotides
Usage¶
stitchRegions(
receptor,
v_seq,
d_seq,
j_seq,
np1_length = "np1_length",
np2_length = "np1_length",
n1_length = "n1_length",
p3v_length = "p3v_length",
p5d_length = "p5d_length",
p3d_length = "p3d_length",
n2_length = "n2_length",
p5j_length = "p5j_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)
- n1_length
- Column name in receptor specifying n1 segment length (experimental)
- p3v_length
- Column name in receptor specifying p3v segment length (experimental)
- p5d_length
- Column name in receptor specifying p5d segment length (experimental)
- p3d_length
- Column name in receptor specifying p3d segment length (experimental)
- n2_length
- Column name in receptor specifying n2 segment length (experimental)
- p5j_length
- Column name in receptor specifying p5j segment length (experimental)
- 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 with segment IDs instead of nucleotides.