reduce_to_field2() is a thin wrapper around the ard.redux() method
(Reduction Type 'lgx' or 'U2') of the
py-ard Python package.
Usage
reduce_to_field2(ard, allele, mode = c("U2", "lgx"))Arguments
- ard
The Python database connection object created by
db_initialize()- allele
A string or character vector with (an) HLA allele(s).
- mode
Reduction mode.
"U2"(default) performs an unambiguous reduction to the equivalent two-field allele."lgx"reduces to the first allele in the group of alleles (often indicated with"g"notation) that is identical to the input allele in the antigen recognition domain (ARD).
Value
A string or character vector of the same length as allele,
with the corresponding two-field alleles.
Details
Uses the IPD-IMGT/HLA database as
initialized with db_initialize(). This function will throw an error if any
of the alleles in the input do not exist in the database. Use
is_in_ipd_db() to safely check if the allele(s) exist(s).
See also
reduce_to_serology() to reduce an allele to
serological equivalents
Examples
if (FALSE) { # \dontrun{
ard <- db_initialize(data_dir = path.expand("~/ipd_db"))
reduce_to_field2(ard, "DQB1*02:02:01")
#> "DQB1*02:02"
reduce_to_field2(ard, "A*01:04:01:01N")
#> "A*01:04N"
# Some alleles return a different result depending on the reduction mode:
reduce_to_field2(ard, "C*07:06", mode = "U2")
#> "C*07:06"
reduce_to_field2(ard, "C*07:06", mode = "lgx")
#> "C*07:01"
# N.B. serology can also be "reduced", but might lead to a long genotype:
reduce_to_field2(ard, "Cw10")
#> "C*03:02/C*03:04Q/C*03:04/C*03:06/C*03:26/C*03:28/C*03:46"
# Also works for vectors:
reduce_to_field2(ard, c("A*01:01:01:01", "A*24:02:01:01"))
#> "A*01:01" "A*24:02"
} # }