resolve_IUPAC_missing {minSNPs}

resolve_IUPAC_missing

Description

resolve_IUPAC_missing is used to replace the ambiguity codes found in the sequences.

Usage

resolve_IUPAC_missing(
  seqc,
  log_operation = TRUE,
  log_file = "replace.log",
  max_ambiguity = -1,
  replace_method = "random",
  N_is_any_base = FALSE,
  output_progress = TRUE,
  bp = MulticoreParam()
)

Arguments

seqc

the sequences to be processed

log_operation

whether to log the operation

log_file

log file to write the operations

max_ambiguity

proportion of ambiguity codes to tolerate, -1 = ignore. Default to -1

replace_method

how to substitute the ambiguity codes, current supported methods:random and most_common, default to "random".

N_is_any_base

whether to treat N as any base or substitute it with one of the alleles found at the position.

output_progress

whether to output progress

bp

the BiocParallel backend

Value

Will return the processed sequences.