find_optimised_snps {minSNPs}

find_optimised_snps

Description

find_optimised_snps is used to find optimised SNPs set.

Usage

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(),
  ...
)

Arguments

seqc

list of sequences, either passed directly from process_allele or read_fasta or equivalence

metric

either 'simpson' or 'percent'

goi

group of interest, if creteria is percent, must be specified, ignored otherwise

accept_multiallelic

whether include positions with > 1 state in goi

number_of_result

number of results to return, 0 will be coerced to 1

max_depth

maximum depth to go before terminating, 0 means it will only calculate the metric for included position

included_positions

included positions

excluded_positions

excluded positions

search_from

search only from these positions, i.e., any positions not in here are excluded, default to NULL

iterate_included

whether to calculate index at each level of the included SNPs

completely_unique

whether to identify completely unique SNPs set, default to FALSE, only the 1st SNP must be different

bp

BiocParallel backend. Rule of thumbs: use MulticoreParam(workers = ncpus - 2)

...

other parameters as needed

Value

Will return the resolution-optimised SNPs set, based on the metric.