subset_model: Subset PHMM Modified from Cameron Nugent's COIL package...

In alexpiper/taxreturn: An R package for retrieving and curating public DNA barcode reference data

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

Description

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

Usage

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.

alexpiper/taxreturn documentation built on Sept. 14, 2024, 7:56 p.m.