Subset PHMM Modified from Cameron Nugent's COIL package https://github.com/CNuge/coil/blob/master/R/subset_PHMM.r

Subset PHMM Modified from Cameron Nugent's COIL package https://github.com/CNuge/coil/blob/master/R/subset_PHMM.r

subset_model(
  x,
  primers = NULL,
  positions = NULL,
  trimprimers = FALSE,
  min_score = 10,
  quiet = FALSE
)

Arguments

x

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

primers

A character vector of length 2 contaning the forward and reverse primer sequences.

positions

A numeric vector of length 2 containing the start and end position for model trimming. Used only if primers = NULL.

trimprimers

logical indicating whether the primer-binding sites should be removed from the sequences in the returned model. Used only if positions = NULL.

min_score

Minimum score for the viterbi alignment.

quiet

Whether to print progress to console.