getGermline - getGermline get germline segment from specified receptor and segment
Description¶
getGermline get germline segment from specified receptor and segment
Usage¶
getGermline(
receptor,
references,
segment,
field,
germ_start,
germ_end,
germ_length,
germ_aa_start,
germ_aa_length,
amino_acid = FALSE
)
Arguments¶
- receptor
- row from AIRR-table containing sequence of interest
- references
- list of reference segments. Must be specific to locus and segment
- segment
- Gene segment to search. Must be V, D, or J.
- field
- Column name for segment gene call (e.g. v_call)
- germ_start
- Column name of index of segment start within germline segment (e.g. v_germline_start)
- germ_end
- Similar to germ_start, but specifies end of segment (e.g. v_germline_end)
- germ_length
- Similar to germ_start, but specifies length of segment (e.g. v_germline_end)
- germ_aa_start
- Column name of index of segment start within germline segment in AA (if amino_acid=TRUE, e.g. v_germline_start)
- germ_aa_length
- Similar to germ_start, but specifies length of segment in AA (if amino_acid=TRUE, e.g. v_germline_end)
- amino_acid
- Perform reconstruction on amino acid sequence (experimental)
Value¶
String of germline sequence from specified segment aligned with the
sequence in the seq column of receptor.