Clean Sequences with PHMM (DEPRECATED)

Clean Sequences with PHMM (DEPRECATED)

clean_seqs(
  x,
  model,
  min_score = 100,
  shave = TRUE,
  maxNs = 0,
  cores = 1,
  quiet = FALSE,
  progress = FALSE
)

Arguments

x

A DNAbin or DNAStringset object

model

A profile hidden Markov model (a "PHMM" object) generated by the aphid R package to align the sequences to.

min_score

The minimum specificity (log-odds score for the optimal alignment) between the query sequence and the PHMM model for the sequence to be retained in the output object.

shave

Whether bases that are outside (to the left or right) of the PHMM object should be shaved from the outputs.

maxNs

The max number of ambiguous N bases to retain

cores

The number of CPUs to parallelize the operation over

quiet

Whether progress should be printed to the console.

progress

Whether a progress bar should be printed.