clean_seqs: Clean Sequences with PHMM (DEPRECATED)

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

Clean Sequences with PHMM (DEPRECATED)

Description

Clean Sequences with PHMM (DEPRECATED)

Usage

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.

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