select_n_set_i_depth: 'select_n_set_i_depth'

In ludwigHoon/minSNPs: Resolution-Optimised SNPs Searcher

select_n_set_i_depth

Description

select_n_set_i_depth is the actual function used to find optimised SNPs set. This function is called by find_optimised_snps, after preprocessing.

Usage

select_n_set_i_depth(
  starting_positions = c(),
  excluded_positions = c(),
  seqc,
  metric,
  number_of_result = 1,
  max_depth = 1,
  seqc_length,
  bp = SerialParam(),
  ...
)

Arguments

starting_positions	the starting positions that is already in the SNP set.
excluded_positions	excluded positions
seqc	list of sequences, either passed directly from process_allele or read_fasta or equivalence
metric	either 'simpson' or 'percent'
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
seqc_length	the length to iterate through.
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.

ludwigHoon/minSNPs documentation built on March 25, 2024, 11:54 a.m.