subsetPHMM: Subset an existing PHMM.

In coil: Contextualization and Evaluation of COI-5P Barcode Data

Subset an existing PHMM.

Description

The subsetPHMM 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

Usage

subsetPHMM(x, start, end)

Arguments

x	an object of class "PHMM" to be subset.
start	The first PHMM position to be inclused in the output PHMM.
end	The last PHMM position to be included in the output PHMM.

Value

an object of class "PHMM"

See Also

derivePHMM

Examples

## subset positions 2-100 of the COI-5P PHMM
short_nt_PHMM <- subsetPHMM(nt_coi_PHMM, 2, 100)

coil documentation built on May 29, 2024, 10:51 a.m.