find_optimised_snps
is used to find optimised SNPs set.
find_optimised_snps(
seqc,
metric = "simpson",
goi = c(),
accept_multiallelic = TRUE,
number_of_result = 1,
max_depth = 1,
included_positions = c(),
excluded_positions = c(),
search_from = NULL,
iterate_included = FALSE,
completely_unique = FALSE,
bp = SerialParam(),
...
)
list of sequences, either passed directly from
process_allele
or read_fasta
or equivalence
either `simpson` or `percent`
group of interest, if creteria is percent, must be specified, ignored otherwise
whether include positions with > 1 state in goi
number of results to return, 0 will be coerced to 1
maximum depth to go before terminating, 0 means it will only calculate the metric for included position
included positions
excluded positions
search only from these positions, i.e., any positions not in here are excluded, default to NULL
whether to calculate index at each level of the included SNPs
whether to identify completely unique SNPs set, default to FALSE, only the 1st SNP must be different
BiocParallel backend. Rule of thumbs: use MulticoreParam(workers = ncpus - 2)
other parameters as needed
Will return the resolution-optimised SNPs set, based on the metric.