subsetPHMM

The <code>subsetPHMM</code> function allows an existing PHMM to be subset
by profile position. This eliminates the need for the training of an additional, smaller
model if query sequences should be compared to only a subsection of an existing PHMM.
The nt_coi_PHMM and aa_coi_PHMM can therefore be subset using this function to constrain
coil's framing and error evaluation to a subset of the COI-5P region

Designed for the cleaning, contextualization and assessment of cytochrome c
oxidase I DNA barcode data (COI-5P, or the five prime portion of COI). It contains
functions for placing COI-5P barcode sequences into a common reading frame,
translating DNA sequences to amino acids and for assessing the likelihood that a
given barcode sequence includes an insertion or deletion error. The error assessment
relies on the comparison of input sequences against nucleotide and amino acid profile
hidden Markov models (PHMMs) (for details see Durbin et al. 1998, ISBN: 9780521629713)
trained on a taxonomically diverse set of reference sequences. The functions are
provided as a complete pipeline and are also available individually for efficient and
targeted analysis of barcode data.

Cameron Nugent

coil

Contextualization and Evaluation of COI-5P Barcode Data

subsetPHMM function

<dl><dt>x</dt>
<dd>an object of class <code>"PHMM"</code> to be subset.</dd>
<dt>start</dt>
<dd>The first PHMM position to be inclused in the output PHMM.</dd>
<dt>end</dt>
<dd>The last PHMM position to be included in the output PHMM.</dd></dl>

Arguments

Subset an existing PHMM. — subsetPHMM

<dl>

<dt>x</dt>
<dd>an object of class <code>"PHMM"</code> to be subset.</dd>


<dt>start</dt>
<dd>The first PHMM position to be inclused in the output PHMM.</dd>


<dt>end</dt>
<dd>The last PHMM position to be included in the output PHMM.</dd>

</dl>

subsetPHMM: Subset an existing PHMM.

Description

Usage

Value

Arguments

See Also

Examples