resolve_IUPAC_missing — resolve_IUPAC

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

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.